Paged similarity queries

An important feature of a database management systems (DBMS) is its client/server architecture, where managing shared memory among the clients and the server is always an tough issue. However, similarity queries are specially sensitive to this kind of architecture, since the answer sizes vary widely. Usually, the answers of similarity query are fully processed to be sent in full to the user, who often is interested in just parts of the answer, e.g. just few elements closer or farther to the query reference. Compelling the DBMS to retrieve the full answer, further ignoring its majority is at least a waste of server processing power. Paging the answer is a technique that splits the answer onto several pages, following client requests. Despite the success of paging on traditional queries, little work has been done to support it in similarity queries. In this work, we present a technique that not only provides paging in similarity range or k-nearest neighbor queries, but also supports them in two variations: the forward similarity query and the backward similarity query. They return elements either increasingly farther of increasingly closer to the query reference. The reported experiments show that, depending on the proportion of the interesting part over the full answer, both techniques allow answering queries much faster than it is obtained in the non-paged way. (C) 2010 Elsevier Inc. All rights reserved.

Seamlessly integrating similarity queries in SQL

Modern database applications are increasingly employing database management systems (DBMS) to store multimedia and other complex data. To adequately support the queries required to retrieve these kinds of data, the DBMS need to answer similarity queries. However, the standard structured query language (SQL) does not provide effective support for such queries. This paper proposes an extension to SQL that seamlessly integrates syntactical constructions to express similarity predicates to the existing SQL syntax and describes the implementation of a similarity retrieval engine that allows posing similarity queries using the language extension in a relational DBM. The engine allows the evaluation of every aspect of the proposed extension, including the data definition language and data manipulation language statements, and employs metric access methods to accelerate the queries. Copyright (c) 2008 John Wiley & Sons, Ltd.

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, bloodbrain barrier and water solubility).

Elementary Petri net inside RFID distributed database (PNRD)

Usually, a Petri net is applied as an RFID model tool. This paper, otherwise, presents another approach to the Petri net concerning RFID systems. This approach, called elementary Petri net inside an RFID distributed database, or PNRD, is the first step to improve RFID and control systems integration, based on a formal data structure to identify and update the product state in real-time process execution, allowing automatic discovery of unexpected events during tag data capture. There are two main features in this approach: to use RFID tags as the object process expected database and last product state identification; and to apply Petri net analysis to automatically update the last product state registry during reader data capture. RFID reader data capture can be viewed, in Petri nets, as a direct analysis of locality for a specific transition that holds in a specific workflow. Following this direction, RFID readers storage Petri net control vector list related to each tag id is expected to be perceived. This paper presents PNRD cornerstones and a PNRD implementation example in software called DEMIS Distributed Environment in Manufacturing Information Systems.

2D QSAR and similarity studies on cruzain inhibitors aimed at improving selectivity over cathepsin L

Hologram quantitative structure-activity relationships (HQSAR) were applied to a data set of 41 cruzain inhibitors. The best HQSAR model (Q(2) = 0.77; R-2 = 0.90) employing Surflex-Sim, as training and test sets generator, was obtained using atoms, bonds, and connections as fragment distinctions and 4-7 as fragment size. This model was then used to predict the potencies of 12 test set compounds, giving satisfactory predictive R-2 value of 0,88. The contribution maps obtained from the best HQSAR model are in agreement with the biological activities of the study compounds. The Trypanosoma cruzi cruzain shares high similarity with the mammalian homolog cathepsin L. The selectivity toward cruzam was checked by a database of 123 compounds, which corresponds to the 41 cruzain inhibitors used in the HQSAR model development plus 82 cathepsin L inhibitors. We screened these compounds by ROCS (Rapid Overlay of Chemical Structures), a Gaussian-shape volume overlap filter that can rapidly identify shapes that match the query molecule. Remarkably, ROCS was able to rank the first 37 hits as being only cruzain inhibitors. In addition, the area under the curve (AUC) obtained with ROCS was 0.96, indicating that the method was very efficient to distinguishing between cruzain and cathepsin L inhibitors. (c) 2007 Elsevier Ltd. All rights reserved.

From the road network database to a graph for localization purposes

The problems of finding best facility locations require complete and accurate road network with the corresponding population data in a specific area. However the data obtained in road network databases usually do not fit in this usage. In this paper we propose our procedure of converting the road network database to a road graph which could be used in localization problems. The road network data come from the National road data base in Sweden. The graph derived is cleaned, and reduced to a suitable level for localization problems. The population points are also processed in ordered to match with that graph. The reduction of the graph is done maintaining most of the accuracy for distance measures in the network.

Information Flow for ALGOL-like Languages

In this paper we present an approach to information flow analysis for a family of languages. We start with a simple imperative language. We present an information flow analysis using a flow logic. The paper contains detailed correctness proofs for this analysis. We next extend the analysis to a restricted form of Idealised Algol, a call-by-value higher-order extension of the simple imperative language (the key restriction being the lack of recursion). The paper concludes with a discussion of further extensions, including a probabilistic extension of Idealised Algol.

Extending Agent Languages for Autonomy

BDI agent languages provide a useful abstraction for complex systems comprised of interactive autonomous entities, but they have been used mostly in the context of single agents with a static plan library of behaviours invoked reactively. These languages provide a theoretically sound basis for agent design but are very limited in providing direct support for autonomy and societal cooperation needed for large scale systems. Some techniques for autonomy and cooperation have been explored in the past in ad hoc implementations, but not incorporated in any agent language. In order to address these shortcomings we extend the well known AgentSpeak(L) BDI agent language to include behaviour generation through planning, declarative goals and motivated goal adoption. We also develop a language-specific multiagent cooperation scheme and, to address potential problems arising from autonomy in a multiagent system, we extend our agents with a mechanism for norm processing leveraging existing theoretical work. These extensions allow for greater autonomy in the resulting systems, enabling them to synthesise new behaviours at runtime and to cooperate in non-scripted patterns.

Development Of Climate Change Information Database And Its Use In Civic Consciousness Enlightenment

GCM outputs such as CMIP3 are available via network access to PCMDI web site. Meteorological researchers are familiar with the usage of the GCM data, but the most of researchers other than meteorology such as agriculture, civil engineering, etc., and general people are not familiar with the GCM. There are some difficulties to use GCM; 1) to download the enormous quantity of data, 2) to understand the GCM methodology, parameters and grids. In order to provide a quick access way to GCM, Climate Change Information Database has been developed. The purpose of the database is to bridge the users and meteorological specialists and to facilitate the understanding the climate changes. The resolution of the data is unified, and climate change amount or factors for each meteorological element are provided from the database. All data in the database are interpolated on the same 80km mesh. Available data are the present-future projections of 27 GCMs, 16 meteorological elements (precipitation, temperature, etc.), 3 emission scenarios (A1B, A2, B1). We showed the summary of this database to residents in Toyama prefecture and measured the effect of showing and grasped the image for the climate change by using the Internet questionary survey. The persons who feel a climate change at the present tend to feel the additional changes in the future. It is important to show the monitoring results of climate change for a citizen and promote the understanding for the climate change that had already occurred. It has been shown that general images for the climate change promote to understand the need of the mitigation, and that it is important to explain about the climate change that might occur in the future even if it did not occur at the present in order to have people recognize widely the need of the adaptation.