A New Nonparametric Pairwise Clustering Algorithm Based on Iterative Estimation of Distance Profiles

We present a novel pairwise clustering method. Given a proximity matrix of pairwise relations (i.e. pairwise similarity or dissimilarity estimates) between data points, our algorithm extracts the two most prominent clusters in the data set. The algorithm, which is completely nonparametric, iteratively employs a two-step transformation on the proximity matrix. The first step of the transformation represents each point by its relation to all other data points, and the second step re-estimates the pairwise distances using a statistically motivated proximity measure on these representations. Using this transformation, the algorithm iteratively partitions the data points, until it finally converges to two clusters. Although the algorithm is simple and intuitive, it generates a complex dynamics of the proximity matrices. Based on this bipartition procedure we devise a hierarchical clustering algorithm, which employs the basic bipartition algorithm in a straightforward divisive manner. The hierarchical clustering algorithm copes with the model validation problem using a general cross-validation approach, which may be combined with various hierarchical clustering methods.We further present an experimental study of this algorithm. We examine some of the algorithm's properties and performance on some synthetic and standard data sets. The experiments demonstrate the robustness of the algorithm and indicate that it generates a good clustering partition even when the data is noisy or corrupted.     

An improved P300-based brain-computer interface.

A brain-computer interface (BCI) is a system for direct communication between brain and computer. The BCI developed in this work is based on a BCI described by Farwell and Donchin in 1988, which allows a subject to communicate one of 36 symbols presented on a 6 x 6 matrix. The system exploits the P300 component of event-related brain potentials (ERP) as a medium for communication. The processing methods distinguish this work from Donchin's work. In this work, independent component analysis (ICA) was used to separate the P300 source from the background noise. A matched filter was used together with averaging and threshold techniques for detecting the existence of P300s. The processing method was evaluated offline on data recorded from six healthy subjects. The method achieved a communication rate of 5.45 symbols/min with an accuracy of 92.1% compared to 4.8 symbols/min with an accuracy of 90% in Donchin's work. The online interface was tested with the same six subjects. The average communication rate achieved was 4.5 symbols/min with an accuracy of 79.5 % as apposed to the 4.8 symbols/min with an accuracy of 56 % in Donchin's work. The presented BCI achieves excellent performance compared to other existing BCIs, and allows a reasonable communication rate, while maintaining a low error rate.     

Atmospheric modulation transfer function in the infrared

In high-resolution ultranarrow field-of-view thermal imagers, image quality over relatively long path lengths is typically limited by atmospheric degradation, especially atmospheric blur. We report our results and analyses of infrared images from two sites, Fort A. P. Hill and Aberdeen Proving Ground. The images are influenced by the various atmospheric phenomena: scattering, absorption, and turbulence. A series of experiments with high-resolution equipment in both the 3-5- and 8-13-microm regions at the two locations indicate that, as in the visible, image quality is limited much more by atmosphere than by the instrumentation for ranges even of the order of only a few kilometers. For paths close to the ground, turbulence is more dominant, whereas for paths involving higher average elevation, aerosol modulation transfer function (MTF) is dominant. As wavelength increases, turbulence MTF also increases, thus permitting aerosol MTF to become more dominant. A critical role in aerosol MTF in the thermal infrared is attributed to absorption, which noticeably decreases atmospheric transmission much more than in the visible, thereby reducing high-spatial-frequency aerosol MTF. These measurements indicate that atmospheric MTF should be a basic component in imaging system design and analysis even in the infrared, especially as higher-resolution hardware becomes available.     

Biblio: automatic meta-data extraction

Biblio is an adaptive system that automatically extracts meta-data from semi-structured and structured scanned documents. Instead of using hand-coded templates or other methods manually customized for each given document format, it uses example-based machine learning to adapt to customer-defined document and meta-data types. We provide results from experiments on the recognition of document information in two document corpuses: a set of scanned journal articles and a set of scanned legal documents. The first set is semi-structured, as the different journals use a variety of flexible layouts. The second set is largely free-form text based on poor quality scans of FAX-quality legal documents. We demonstrate accuracy on the semi-structured document set roughly comparable to hand-coded systems, and much worse performance on the legal documents.     

Hansenula polymorpha Pex1p and Pex6p are peroxisome‐associated AAA proteins that functionally and physically interact

We have cloned the Hansenula polymorpha PEX1 and PEX6 genes by functional complementation of the corresponding peroxisome‐deficient (pex) mutants. The gene products, HpPex1p and HpPex6p, are ATPases which both belong to the AAA protein family. Cells deleted for either gene (Δpex1 or Δpex6) were characterized by the presence of small peroxisomal remnants which contained peroxisomal membrane proteins and minor amounts of matrix proteins. The bulk of the matrix proteins, however, resided in the cytosol. In cell fractionation studies HpPex1p and HpPex6p co‐sedimented with the peroxisomal membrane protein HpPex3p in both wild‐type cells and in Δpex4, Δpex8 or Δpex14 cells. Both proteins are loosely membrane‐bound and face the cytosol. Furthermore, HpPex1p and HpPex6p physically and functionally interact in vivo. Overexpression of PEX6 resulted in defects in peroxisomal matrix protein import. By contrast, overexpression of PEX1 was not detrimental to the cells. Interestingly, co‐overproduction of HpPex1p rescued the protein import defect caused by HpPex6p overproduction. Overproduced HpPex1p and HpPex6p remained predominantly membrane‐bound, but only partially co‐localized with the peroxisomal membrane protein HpPex3p. Our data indicate that HpPex1p and HpPex6p function in a protein complex associated with the peroxisomal membrane and that overproduced, mislocalized HpPex6p prevents HpPex1p from reaching its site of activity. Copyright © 1999 John Wiley & Sons, Ltd.     

Fast and robust multiframe super resolution

Super-resolution reconstruction produces one or a set of high-resolution images from a set of low-resolution images. In the last two decades, a variety of super-resolution methods have been proposed. These methods are usually very sensitive to their assumed model of data and noise, which limits their utility. This paper reviews some of these methods and addresses their short-comings. We propose an alternate approach using L1 norm minimization and robust regularization based on a bilateral prior to deal with different data and noise models. This computationally inexpensive method is robust to errors in motion and blur estimation and results in images with sharp edges. Simulation results confirm the effectiveness of our method and demonstrate its superiority to other super-resolution methods.     

A Variational Framework for Retinex

Retinex theory addresses the problem of separating the illumination from the reflectance in a given image and thereby compensating for non-uniform lighting. This is in general an ill-posed problem. In this paper we propose a variational model for the Retinex problem that unifies previous methods. Similar to previous algorithms, it assumes spatial smoothness of the illumination field. In addition, knowledge of the limited dynamic range of the reflectance is used as a constraint in the recovery process. A penalty term is also included, exploiting a-priori knowledge of the nature of the reflectance image. The proposed formulation adopts a Bayesian view point of the estimation problem, which leads to an algebraic regularization term, that contributes to better conditioning of the reconstruction problem.Based on the proposed variational model, we show that the illumination estimation problem can be formulated as a Quadratic Programming optimization problem. An efficient multi-resolution algorithm is proposed. It exploits the spatial correlation in the reflectance and illumination images. Applications of the algorithm to various color images yield promising results.     

Materials Modelling of π-Phase Monochalcogenides

The π-phase monochalcogenides are a recently discovered new family of cubic semiconductors with band gaps in the infrared. Unusually, they consist of a low-symmetry, non-centrosymmetric 64 atom simple cubic unit cell and thus may be expected to present exceptional physical properties. Furthermore, they have been obtained only in nanometric form, which raises questions concerning their thermodynamic stability. In a series of studies over the last three years, the authors and others have attempted to unravel the nature and properties of this family of materials through ab-initio materials modelling. An integrated overview of these works is presented here.     

Electronic structure study of ordering and interfacial interaction in graphene/Cu composites

Graphene CVD-grown on Cu has been studied using Raman spectroscopy, X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES). Raman data indicate the presence of weak compressive strain at the interface of graphene/Cu. Compared with highly ordered pyrolytic graphite (HOPG), new electronic states in the conduction band are observed for graphene/Cu, which are mainly ascribed to the defect states and interfacial interaction between the single graphene layer and Cu surface. Moreover, polarization dependent XAS measurements demonstrate that the graphene/Cu exhibits a high degree of alignment and weak corrugation on the surface. Significant intensity modulation in the resonant XES spectral shape upon different excitation energies near the C K-edge indicates that graphene layer preserves an intrinsic momentum as that of HOPG and the interaction between graphene and Cu shows weak influence on the valence band structure of graphene. However, broad inelastic features and subtle peak shifts are observed in the resonant XES spectra of graphene/Cu in comparison of HOPG, which can be mainly attributed to the electron–phonon scattering and charge transfer from the interfacial interaction of graphene and Cu substrate.     

WIP Remodeling Actin behind the Scenes: How WIP Reshapes Immune and Other Functions

Actin polymerization is a fundamental cellular process regulating immune cell functions and the immune response. The Wiskott-Aldrich syndrome protein (WASp) is an actin nucleation promoting factor, which is exclusively expressed in hematopoietic cells, where it plays a key regulatory role in cytoskeletal dynamics. WASp interacting protein (WIP) was first discovered as the binding partner of WASp, through the use of the yeast two hybrid system. WIP was later identified as a chaperone of WASp, necessary for its stability. Mutations occurring at the WASp homology 1 domain (WH1), which serves as the WIP binding site, were found to cause the Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT). WAS manifests as an immune deficiency characterized by eczema, thrombocytopenia, recurrent infections, and hematopoietic malignancies, demonstrating the importance of WIP for WASp complex formation and for a proper immune response. WIP deficiency was found to lead to different abnormalities in the activity of various lymphocytes, suggesting differential cell-dependent roles for WIP. Additionally, WIP deficiency causes cellular abnormalities not found in WASp-deficient cells, indicating that WIP fulfills roles beyond stabilizing WASp. Indeed, WIP was shown to interact with various binding partners, including the signaling proteins Nck, CrkL and cortactin. Recent studies have demonstrated that WIP also takes part in non immune cellular processes such as cancer invasion and metastasis, in addition to cell subversion by intracellular pathogens. Understanding of numerous functions of WIP can enhance our current understanding of activation and function of immune and other cell types.