Hybrid model predictive control for freeway traffic using discrete speed limit signals

HYCON2 Show day - Traffic modeling, Estimation and Control 13/05/2014 GrenobleIn this paper, two hybrid Model Predictive Control (MPC) approaches for freeway traffic control are proposed considering variable speed limits (VSL) as discrete variables as in current real world implementations. These discrete characteristics of the speed limits values and some necessary constraints for the actual operation of VSL are usually underestimated in the literature, so we propose a way to include them using a macroscopic traffic model within an MPC framework. For obtaining discrete signals, the MPC controller has to solve a highly non-linear optimization problem, including mixed-integer variables. Since solving such a problem is complex and difficult to execute in real-time, we propose some methods to obtain reasonable control actions in a limited computation time. The first two methods (-exhaustive and -genetic discretization) consist of first relaxing the discrete constraints for the VSL inputs; and then, based on this continuous solution and using a genetic or an exhaustive algorithm, to find discrete solutions within a distance of the continuous solution that provide a good performance. The second class of methods split the problem in a continuous optimization for the ramp metering signals and in a discrete optimization for speed limits. The speed limits optimization, which is much more time-consuming than the ramp metering one, is solved by a genetic or an exhaustive algorithm in communication with a non-linear solver for the ramp metering. The proposed methods are tested by simulation, showing not only a good performance, but also keeping the computation time reduced.Unión Europea FP7/2007–201

Genome-wide inference of ancestral recombination graphs

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of n chromosomes conditional on an ARG of n-1 chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the true posterior distribution and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. Preliminary results also indicate that our methods can be used to gain insight into complex features of human population structure, even with a noninformative prior distribution.Comment: 88 pages, 7 main figures, 22 supplementary figures. This version contains a substantially expanded genomic data analysi

Parameter estimation for Boolean models of biological networks

Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network models based on experimental data and biological input. The key feature is a discrete analog of parameter estimation for continuous models. With only experimental data as input, the software can be used as a tool for reverse-engineering of Boolean network models from experimental time course data.Comment: Web interface of the software is available at http://polymath.vbi.vt.edu/polynome