Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors

Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort

Text mining with the WEBSOM

The emerging field of text mining applies methods from data mining and exploratory data analysis to analyzing text collections and to conveying information to the user in an intuitive manner. Visual, map-like displays provide a powerful and fast medium for portraying information about large collections of text. Relationships between text items and collections, such as similarity, clusters, gaps and outliers can be communicated naturally using spatial relationships, shading, and colors. In the WEBSOM method the self-organizing map (SOM) algorithm is used to automatically organize very large and high-dimensional collections of text documents onto two-dimensional map displays. The map forms a document landscape where similar documents appear close to each other at points of the regular map grid. The landscape can be labeled with automatically identified descriptive words that convey properties of each area and also act as landmarks during exploration. With the help of an HTML-based interactive tool the ordered landscape can be used in browsing the document collection and in performing searches on the map. An organized map offers an overview of an unknown document collection helping the user in familiarizing herself with the domain. Map displays that are already familiar can be used as visual frames of reference for conveying properties of unknown text items. Static, thematically arranged document landscapes provide meaningful backgrounds for dynamic visualizations of for example time-related properties of the data. Search results can be visualized in the context of related documents. Experiments on document collections of various sizes, text types, and languages show that the WEBSOM method is scalable and generally applicable. Preliminary results in a text retrieval experiment indicate that even when the additional value provided by the visualization is disregarded the document maps perform at least comparably with more conventional retrieval methods.reviewe

An empirical study of inter-concept similarities in multimedia ontologies

Generic concept detection has been a widely studied topic in recent research on multimedia analysis and retrieval, but the issue of how to exploit the structure of a multimedia ontology as well as different inter-concept relations, has not received similar attention. In this paper, we present results from our empirical analysis of different types of similarity among semantic concepts in two multimedia ontologies, LSCOM-Lite and CDVP-206. The results show promise that the proposed methods may be helpful in providing insight into the existing inter-concept relations within an ontology and selecting the most facilitating set of concepts and hierarchical relations. Such an analysis as this can be utilized in various tasks such as building more reliable concept detectors and designing large-scale ontologies

K-Space at TRECVID 2008

In this paper we describe K-Space’s participation in TRECVid 2008 in the interactive search task. For 2008 the K-Space group performed one of the largest interactive video information retrieval experiments conducted in a laboratory setting. We had three institutions participating in a multi-site multi-system experiment. In total 36 users participated, 12 each from Dublin City University (DCU, Ireland), University of Glasgow (GU, Scotland) and Centrum Wiskunde and Informatica (CWI, the Netherlands). Three user interfaces were developed, two from DCU which were also used in 2007 as well as an interface from GU. All interfaces leveraged the same search service. Using a latin squares arrangement, each user conducted 12 topics, leading in total to 6 runs per site, 18 in total. We officially submitted for evaluation 3 of these runs to NIST with an additional expert run using a 4th system. Our submitted runs performed around the median. In this paper we will present an overview of the search system utilized, the experimental setup and a preliminary analysis of our results

K-Space at TRECVid 2008

In this paper we describe K-Space’s participation in TRECVid 2008 in the interactive search task. For 2008 the K-Space group performed one of the largest interactive video information retrieval experiments conducted in a laboratory setting. We had three institutions participating in a multi-site multi-system experiment. In total 36 users participated, 12 each from Dublin City University (DCU, Ireland), University of Glasgow (GU, Scotland) and Centrum Wiskunde & Informatica (CWI, the Netherlands). Three user interfaces were developed, two from DCU which were also used in 2007 as well as an interface from GU. All interfaces leveraged the same search service. Using a latin squares arrangement, each user conducted 12 topics, leading in total to 6 runs per site, 18 in total. We officially submitted for evaluation 3 of these runs to NIST with an additional expert run using a 4th system. Our submitted runs performed around the median. In this paper we will present an overview of the search system utilized, the experimental setup and a preliminary analysis of our results

PERSIANN-MSA: A precipitation estimation method from satellite-based multispectral analysis

Visible and infrared data obtained from instruments onboard geostationary satellites have been extensively used for monitoring clouds and their evolution. The Advanced Baseline Imager (ABI) that will be launched onboard the Geostationary Operational Environmental Satellite-R (GOES-R) series in the near future will offer a larger range of spectral bands; hence, it will provide observations of cloud and rain systems at even finer spatial, temporal, and spectral resolutions than are possible with the current GOES. In this paper, a new method called Precipitation Estimation from Remotely Sensed information using Artificial Neural Networks-Multispectral Analysis (PERSIANN-MSA) is proposed to evaluate the effect of using multispectral imagery on precipitation estimation. The proposed approach uses a self-organizing feature map (SOFM) to classify multidimensional input information, extracted from each grid box and corresponding textural features of multispectral bands. In addition, principal component analysis (PCA) is used to reduce the dimensionality to a few independent input features while preserving most of the variations of all input information. The above method is applied to estimate rainfall using multiple channels of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) onboard the Meteosat Second Generation (MSG) satellite. In comparison to the use of a single thermal infrared channel, the analysis shows that using multispectral data has the potential to improve rain detection and estimation skills with an average of more than 50% gain in equitable threat score for rain/no-rain detection, and more than 20% gain in correlation coefficient associated with rain-rate estimation. © 2009 American Meteorological Society