Generalized Simulated Annealing

Many problems in mathematics, statistics, finance, biology, pharmacology, physics, applied mathematics, economics, and chemistry involve the determination of the global minimum of multidimensional real‐valued functions. Simulated annealing methods have been widely used for different global optimization problems. Multiple versions of simulated annealing have been developed, including classical simulated annealing (CSA), fast simulated annealing (FSA), and generalized simulated annealing (GSA). After revisiting the basic idea of GSA using Tsallis statistics, we implemented a modified GSA approach using the R package GenSA. This package was designed to solve complicated nonlinear objective functions with a large number of local minima. In this chapter, we provide a brief introduction to this R package and demonstrate its utility by solving non‐convexoptimization problems in different fields: physics, environmental science, and finance. We performed a comprehensive comparison between GenSA and other widely used R packages, including rgenoud and DEoptim. GenSA is useful and can provide a solution that is comparable with or even better than that provided by other widely used R packages for optimization

Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract

Mucociliary clearance (MCC), considered as a collaboration of mucus secreted from goblet cells, the airway surface liquid layer, and the beating of cilia of ciliated cells, is the airways’ defense system against airborne contaminants. Because the process is well described at the molecular level, we gathered the available information into a suite of comprehensive causal biological network (CBN) models. The suite consists of three independent models that represent (1) cilium assembly, (2) ciliary beating, and (3) goblet cell hyperplasia/metaplasia and that were built in the Biological Expression Language, which is both human-readable and computable. The network analysis of highly connected nodes and pathways demonstrated that the relevant biology was captured in the MCC models. We also show the scoring of transcriptomic data onto these network models and demonstrate that the models capture the perturbation in each dataset accurately. This work is a continuation of our approach to use computational biological network models and mathematical algorithms that allow for the interpretation of high-throughput molecular datasets in the context of known biology. The MCC network model suite can be a valuable tool in personalized medicine to further understand heterogeneity and individual drug responses in complex respiratory diseases

"From song of birds to extended virtual reed instruments": Physical Modeling of Birds' Vocal Tracks and Application to a New Kind of Sound Sustain Virtual Instruments

International audienceThe vocal tracks o animals show a wide variety of sound generation processes. They present similarity with human vocal track but they are sometimes rather different. In order to find new physical models for synthesis and control of musical sounds, we have studied and built models of the vocal track of birds. A bird has to produce sound (as a means to indicate the localization and territory to the others) with a great acoustical efficiency, in comparison to its size. Moreover, the vocal track of birds, the syrinx, has an interesting characteristic : it is composed of two pipes receiving the air flow from the lung, linked to the trachea. the air flow produces an excitation of the "membrane tympaniforme" (the analog of the human vocal sting) and the difference of the two air pressures in these pipes gives a very characteristic way to control the sound. Using the CORDIS-ANIMA physical modeling language developed at ACROE, we achieved in our laboratory. Then, we introduced the two pipes as two air flows. We introduced also two types of muscular action : the control of the air flow through bronchi, and the contro of the membrane action. From this basic model, il is possible to developed extended models in several ways, allowing timbre mutation"from the bird to the clarinet". but mainly, it is possible to set a new range of gesture performance exploration within virtual instruments : using a force-feedback interface, we can sing with our fingers, like (or unlike) the birds