Face authentication with Gabor information on deformable graphs
Elastic graph matching has been proposed as a practical implementation of dynamic link matching, which is a neural network with dynamically evolving links between a reference model and an input image. Each node of the graph contains features that characterize the neighborhood of its location in the image. The elastic graph matching usually consists of two consecutive steps, namely a matching with a rigid grid, followed by a deformation of the grid, which is actually the elastic part. The deformation step is introduced in order to allow for some deformation, rotation, and scaling of the object to be matched. This method is applied here to the authentication of human faces where candidates claim an identity that is to be checked. The matching error as originally suggested is not powerful enough to provide satisfying results in this case. We introduce an automatic weighting of the nodes according to their significance. We also explore the significance of the elastic deformation for an application of face-based person authentication. We compare performance results obtained with and without the second matching step. Results show that the deformation step slightly increases the performance, but has lower influence than the weighting of the nodes. The best results are obtained with the combination of both aspects. The results provided by the proposed method compare favorably with two methods that require a prior geometric face normalization, namely the synergetic and eigenface approaches.

title: Expert Conciliation for Multi Modal Person Authentication Systems by Bayesian Statistics
abstract: We present an algorithm functioning as a supervisor module in a multi expert decision making machine. It uses the Bayes theory in order to estimate the biases of individual expert opinions. These are then used to calibrate and conciliate expert opinions to one opinion. We present a framework for simulating decision strategies using expert opinions whose properties are easily modifiable. By using real data coming from a person authentication system using image and speech data we were able to confirm that the proposed supervisor improves the quality of individual expert decisions by reaching success rates of 99.5 %.

title: Graph Edit Distance with Node Splitting and Merging, and Its Application to Diatom Idenfication
abstract: A new graph matching scheme based on an extended set of edit operations, which include the splitting and merging of nodes, is proposed in this paper. This scheme is useful in applications where the nodes of the considered graphs represent regions extracted by some segmentation procedure from an image. To demonstrate the feasibility of the proposed method, its application to the automatic identification of diatoms (unicellular algae) is described.

title: Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins
abstract: In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson--Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson--Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization-based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor.

title: Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
abstract: The prediction of a ligand binding constant requires generating three-dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine-like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal-gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root-mean-square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H-bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands.

title: Identification of Diatoms by Grid Graph Matching
abstract: Diatoms are unicellular algae found in water and other places wherever there is humidity and enough light for photo synthesis. In this paper a graph matching based identification approach for the retrieval of diatoms from an image database is presented. The retrieval is based on the matching of labeled grid graphs carrying texture information of the underlying diatom. A grid graph is a regular, rectangular arrangement of nodes overlaid on an image. Each node of the graph is labeled with texture features describing a rectangular sub-region of the object. Properties of gray level co-occurrence matrices as well as of Gabor wavelets are used as texture features. The method has been evaluated on a diatom database holding images of 188 different diatoms belonging to 38 classes. For the identification of these diatoms recognition rates of more than 90 percent were obtained.

title: How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin
abstract: The rate constant of an enzyme-catalysed reaction is one of the major target properties to understand protein function. Atomic-detail computer simulations can in principle be used to estimate rate constants from the energy profile along the reaction coordinate. For such simulations, molecular mechanics is combined with a quantum description of the reaction process. In molecular mechanics calculations, the electrostatic field is represented by the Coulomb potential of partial atomic charges which have been parametrised for small building blocks in vacuum and transferred to the macromolecule. In aqueous solution, however, the electrostatic interactions are affected by the solvent polarization. While this can be described by numerically solving the Poisson-Boltzmann equation, it is computationally expensive. A simple approximation to this is to optimally reproduce the electrostatic potential in solution by reparametrising the partial atomic charges in such a way that a simple Coulomb potential can still be used. Such a procedure would allow to perform fast calculations of reaction processes in proteins while accounting for the solvent screening effect. Here, this method is tested on myosin, a motor protein that is both an enzyme and exists in very different conformations.