Waiting time distributions for pattern occurrence in a constrained sequence

Analysis of Algorithm

On the first k moments of the random count of a pattern in a multi-states sequence generated by a Markov source

In this paper, we develop an explicit formula allowing to compute the first k moments of the random count of a pattern in a multi-states sequence generated by a Markov source. We derive efficient algorithms allowing to deal both with low or high complexity patterns and either homogeneous or heterogenous Markov models. We then apply these results to the distribution of DNA patterns in genomic sequences where we show that moment-based developments (namely: Edgeworth's expansion and Gram-Charlier type B series) allow to improve the reliability of common asymptotic approximations like Gaussian or Poisson approximations

How to read probability distributions as statements about process

Probability distributions can be read as simple expressions of information. Each continuous probability distribution describes how information changes with magnitude. Once one learns to read a probability distribution as a measurement scale of information, opportunities arise to understand the processes that generate the commonly observed patterns. Probability expressions may be parsed into four components: the dissipation of all information, except the preservation of average values, taken over the measurement scale that relates changes in observed values to changes in information, and the transformation from the underlying scale on which information dissipates to alternative scales on which probability pattern may be expressed. Information invariances set the commonly observed measurement scales and the relations between them. In particular, a measurement scale for information is defined by its invariance to specific transformations of underlying values into measurable outputs. Essentially all common distributions can be understood within this simple framework of information invariance and measurement scale.Comment: v2: added table of contents, adjusted section numbers v3: minor editing, updated referenc

Long term monitoring of mode switching for PSR B0329+54

The mode switching phenomenon of PSR B0329+54 is investigated based on the long-term monitoring from September 2003 to April 2009 made with the Urumqi 25m radio telescope at 1540 MHz. At that frequency, the change of relative intensity between the leading and trailing components is the predominant feature of mode switching. The intensity ratios between the leading and trailing components are measured for the individual profiles averaged over a few minutes. It is found that the ratios follow normal distributions, where the abnormal mode has a wider typical width than the normal mode, indicating that the abnormal mode is less stable than the normal mode. Our data show that 84.9% of the time for PSR B0329+54 was in the normal mode and 15.1% was in the abnormal mode. From the two passages of eight-day quasi-continuous observations in 2004, and supplemented by the daily data observed with 15 m telescope at 610 MHz at Jodrell Bank Observatory, the intrinsic distributions of mode timescales are constrained with the Bayesian inference method. It is found that the gamma distribution with the shape parameter slightly smaller than 1 is favored over the normal, lognormal and Pareto distributions. The optimal scale parameters of the gamma distribution is 31.5 minutes for the abnormal mode and 154 minutes for the normal mode. The shape parameters have very similar values, i.e. 0.75^{+0.22}_{-0.17} for the normal mode and 0.84^{+0.28}_{-0.22} for the abnormal mode, indicating the physical mechanisms in both modes may be the same. No long-term modulation of the relative intensity ratios was found for both the modes, suggesting that the mode switching was stable. The intrinsic timescale distributions, for the first time constrained for this pulsar, provide valuable information to understand the physics of mode switching.Comment: 31 pages,12 figures, Accepted by the Ap

Moments of the Count of a Regular Expression in a Heterogeneous Random Sequence

International audienceWe focus here on the distribution of the random count N of a regular expression in a multi-state random sequence generated by a heterogenous Markov source. We first briefly recall how classical Markov chain embedding techniques allow reducing the problem to the count of specific transitions in a (heterogenous) order 1 Markov chain over a deterministic finite automaton state space. From this result we derive the expression of both the mgf/pgf of N as well as the factorial and non-factorial moments of N. We then introduce the notion of evidence-based constraints in this context. Following the classical forward/backward algorithm in hidden Markov models, we provide explicit recursions allowing to compute the mgf/pgf of N under the evidence constraint. All the results presented are illustrated with a toy example

Stochastic surgery selection and sequencing under dynamic emergency break-ins

Anticipating the impact of urgent emergency arrivals on operating room schedules remains methodologically and computationally challenging. This paper investigates a model for surgery scheduling, in which both surgery durations and emergency patient arrivals are stochastic. When an emergency patient arrives he enters the first available room. Given the sets of surgeries available to each operating room for that day, as well as the distributions of the main stochastic variables, we aim to find the per-room surgery sequences that minimise a joint objective, which includes over- and under-utilisation, the amount of cancelled patients, as well as the risk that emergencies suffer an excessively long waiting time. We show that a detailed analysis of emergency break-ins and their disruption of the schedule leads to a lower total cost compared to less sophisticated models. We also map the trade-off between the threshold for excessive waiting time, and the set of other objectives. Finally, an efficient heuristic is proposed to accurately estimate the value of a solution with significantly less computational effort.Anticipating the impact of urgent emergency arrivals on operating room schedules remains methodologically and computationally challenging. This paper investigates a model for surgery scheduling, in which both surgery durations and emergency patient arrivals are stochastic. When an emergency patient arrives he enters the first available room. Given the sets of surgeries available to each operating room for that day, as well as the distributions of the main stochastic variables, we aim to find the per-room surgery sequences that minimise a joint objective, which includes over- and under-utilisation, the amount of cancelled patients, as well as the risk that emergencies suffer an excessively long waiting time. We show that a detailed analysis of emergency break-ins and their disruption of the schedule leads to a lower total cost compared to less sophisticated models. We also map the trade-off between the threshold for excessive waiting time, and the set of other objectives. Finally, an efficient heuristic is proposed to accurately estimate the value of a solution with significantly less computational effort.A

Evolution of new regulatory functions on biophysically realistic fitness landscapes

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous avoidance of deleterious "crosstalk" with non-cognate molecules? Although physical models of molecular interactions provide a framework in which co-evolution of network components can be analyzed, most theoretical studies have focused on the evolution of individual alleles, neglecting the network. In contrast, we study the elementary step in the evolution of gene regulatory networks: duplication of a transcription factor followed by selection for TFs to specialize their inputs as well as the regulation of their downstream genes. We show how to coarse grain the complete, biophysically realistic genotype-phenotype map for this process into macroscopic functional outcomes and quantify the probability of attaining each. We determine which evolutionary and biophysical parameters bias evolutionary trajectories towards fast emergence of new functions and show that this can be greatly facilitated by the availability of "promiscuity-promoting" mutations that affect TF specificity