Recognition of specific functionally-important DNA sequence fragments is considered one of the most important problems in bioinformatics. One type of such fragments are promoters, i.e., short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. In this paper, Support Vector Machine (SVM) is used for classificat...

The thermal and optical properties of multilayered dental tissue structure, the result of the surface-grown prismless layer on enamel, were evaluated simultaneously using multiparameter fits of photothermal radiometry frequency responses. The photothermal field generated in a tooth sample with near-infrared laser excitation was described using a coupled diffuse-photon-density and thermal wave m...

BioPSE is a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. BioPSE can be envisioned as a “computational workbench,” in which a scientist can design and modify simulations interactively via a dataflow programming model. As opposed to the typical “off-line” simulation mode (in which the scientist manuall...

We develop a method and a computer code for the systematic optimization of a transferable tight-binding model for carbon-hydrogen compounds. We take as reference a density-functional theory calculation in the local density approximation and, using a «downhill simplex» routine, we minimize the squared difference between the energies predicted by the reference model and those obtained with our ti...

We address a challenge of active flow control: the optimization many actuation parameters guaranteeing fast convergence and avoiding suboptimal local minima. This is addressed by new optimizer, called explorative gradient method (EGM). EGM alternatively performs one exploitive downhill simplex step an Latin hypercube sampling iteration. Thus, rate based guaranteed while, at same time, better mi...

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair d...

A general hill-climbing attack to biometric systems based on a modification of the downhill simplex algorithm is presented. The scores provided by the matcher are used in this approach to adapt iteratively an initial estimate of the attacked template to the specificities of the client being attacked. The proposed attack is evaluated on a competitive feature-based signature verification system o...

A recent paper described a new machine translation evaluation metric, AMBER. This paper describes two changes to AMBER. The first one is incorporation of a new ordering penalty; the second one is the use of the downhill simplex algorithm to tune the weights for the components of AMBER. We tested the impact of the two changes, using data from the WMT metrics task. Each of the changes by itself i...

A photonic crystal fiber is optimized for chromatic dispersion compensation by using inner cladding modes. To this end, a photonic-oriented version of the downhill-simplex algorithm is employed. The numerical results show a dispersion profile that accurately compensates the targeted dispersion curve, as well as its dispersion slope. The presented fiber has a simple structure, while radiation lo...