The transposition median problem is NP-complete

During recent years, the genomes of more and more species have been sequenced, providing data for phylogenetic reconstruction based on genome rearrangement measures, where the most important distance measures are the reversal distance and the transposition distance. The two main tasks in all phylogenetic reconstruction algorithms are to calculate pairwise distances and to solve the median of three problem. While the reversal distance problem can be solved in linear time, the reversal median problem has been proven to be NP-complete. The status of the transposition distance problem is still open, but it is conjectured to be more difficult than the reversal problem. This, in turn, also suggests that the transposition median problem is NP-complete. However, this conjecture could not yet be proven. We have now succeeded in giving a non-trivial proof for the NP-completeness of the transposition median problem.     

An algorithmic framework for network reconstruction

Models of biological systems and phenomena are of high scientific interest and practical relevance, but not always easy to obtain due to their inherent complexity. To gain the required insight, experimental data are provided and need to be interpreted in terms of models that explain the observed phenomena. In systems biology the framework of Petri nets is often used to describe models for the regulatory mechanisms of biological systems. The aim of this paper is to provide, based on results in Marwan et al. (2008) [1] and Durzinsky et al. (2008) [2], an algorithmic framework for the challenging task of generating all possible Petri nets fitting the given experimental data.     

Temporal Kohonen Map and the Recurrent Self-Organizing Map: Analytical and Experimental Comparison

This paper compares two Self-Organizing Map (SOM) based models for temporal sequence processing (TSP) both analytically and experimentally. These models, Temporal Kohonen Map (TKM) and Recurrent Self-Organizing Map (RSOM), incorporate leaky integrator memory to preserve the temporal context of the input signals. The learning and the convergence properties of the TKM and RSOM are studied and we show analytically that the RSOM is a significant improvement over the TKM, because the RSOM allows simple derivation of a consistent learning rule. The results of the analysis are demonstrated with experiments.     

Evolving Teams of Predictors with Linear Genetic Programming

This paper applies the evolution of GP teams to different classification and regression problems and compares different methods for combining the outputs of the team programs. These include hybrid approaches where (1) a neural network is used to optimize the weights of programs in a team for a common decision and (2) a realnumbered vector (the representation of evolution strategies) of weights is evolved with each term in parallel. The cooperative team approach results in an improved training and generalization performance compared to the standard GP method. The higher computational overhead of team evolution is counteracted by using a fast variant of linear GP.     

Interactive volume exploration for feature detection and quantification in industrial CT data

This paper presents a novel method for interactive exploration of industrial CT volumes such as cast metal parts, with the goal of interactively detecting, classifying, and quantifying features using a visualization-driven approach. The standard approach for defect detection builds on region growing, which requires manually tuning parameters such as target ranges for density and size, variance, as well as the specification of seed points. If the results are not satisfactory, region growing must be performed again with different parameters. In contrast, our method allows interactive exploration of the parameter space, completely separated from region growing in an unattended pre-processing stage. The pre-computed feature volume tracks a feature size curve for each voxel over time, which is identified with the main region growing parameter such as variance. A novel 3D transfer function domain over (density, feature size, time) allows for interactive exploration of feature classes. Features and feature size curves can also be explored individually, which helps with transfer function specification and allows coloring individual features and disabling features resulting from CT artifacts. Based on the classification obtained through exploration, the classified features can be quantified immediately.     

3D Video Billboard Clouds

3D video billboard clouds reconstruct and represent a dynamic three-dimensional scene using displacement-mapped billboards. They consist of geometric proxy planes augmented with detailed displacement maps and combine the generality of geometry-based 3D video with the regularization properties of image-based 3D video. 3D video billboards are an image-based representation placed in the disparity space of the acquisition cameras and thus provide a regular sampling of the scene with a uniform error model. We propose a general geometry filtering framework which generates time-coherent models and removes reconstruction and quantization noise as well as calibration errors. This replaces the complex and time-consuming sub-pixel matching process in stereo reconstruction with a bilateral filter. Rendering is performed using a GPU-accelerated algorithm which generates consistent view-dependent geometry and textures for each individual frame. In addition, we present a semi-automatic approach for modeling dynamic three-dimensional scenes with a set of multiple 3D video billboards clouds.     

Local statistics of retinal optic flow for self-motion through natural sceneries

Image analysis in the visual system is well adapted to the statistics of natural scenes. Investigations of natural image statistics have so far mainly focused on static features. The present study is dedicated to the measurement and the analysis of the statistics of optic flow generated on the retina during locomotion through natural environments. Natural locomotion includes bouncing and swaying of the head and eye movement reflexes that stabilize gaze onto interesting objects in the scene while walking. We investigate the dependencies of the local statistics of optic flow on the depth structure of the natural environment and on the ego-motion parameters. To measure these dependencies we estimate the mutual information between correlated data sets. We analyze the results with respect to the variation of the dependencies over the visual field, since the visual motions in the optic flow vary depending on visual field position. We find that retinal flow direction and retinal speed show only minor statistical interdependencies. Retinal speed is statistically tightly connected to the depth structure of the scene. Retinal flow direction is statistically mostly driven by the relation between the direction of gaze and the direction of ego-motion. These dependencies differ at different visual field positions such that certain areas of the visual field provide more information about ego-motion and other areas provide more information about depth. The statistical properties of natural optic flow may be used to tune the performance of artificial vision systems based on human imitating behavior, and may be useful for analyzing properties of natural vision systems.     

Low-cost telepresence for collaborative virtual environments

We present a novel low-cost method for visual communication and telepresence in a CAVEtrade-like environment, relying on 2D stereo-based video avatars. The system combines a selection of proven efficient algorithms and approximations in a unique way, resulting in a convincing stereoscopic real-time representation of a remote user acquired in a spatially immersive display. The system was designed to extend existing projection systems with acquisition capabilities requiring minimal hardware modifications and cost. The system uses infrared-based image segmentation to enable concurrent acquisition and projection in an immersive environment without a static background. The system consists of two color cameras and two additional b/w cameras used for segmentation in the near-IR spectrum. There is no need for special optics as the mask and color image are merged using image-warping based on a depth estimation. The resulting stereo image stream is compressed, streamed across a network, and displayed as a frame-sequential stereo texture on a billboard in the remote virtual environment