Quantitative pharmacophore models with inductive logic programming

Three-dimensional models, or pharmacophores, describing Euclidean constraints on the location on small molecules of functional groups (like hydrophobic groups, hydrogen acceptors and donors, etc.), are often used in drug design to describe the medicinal activity of potential drugs (or ‘ligands’). This medicinal activity is produced by interaction of the functional groups on the ligand with a binding site on a target protein. In identifying structure-activity relations of this kind there are three principal issues: (1) It is often difficult to “align” the ligands in order to identify common structural properties that may be responsible for activity; (2) Ligands in solution can adopt different shapes (or `conformations’) arising from torsional rotations about bonds. The 3-D molecular substructure is typically sought on one or more low-energy conformers; and (3) Pharmacophore models must, ideally, predict medicinal activity on some quantitative scale. It has been shown that the logical representation adopted by Inductive Logic Programming (ILP) naturally resolves many of the difficulties associated with the alignment and multi-conformation issues. However, the predictions of models constructed by ILP have hitherto only been nominal, predicting medicinal activity to be present or absent. In this paper, we investigate the construction of two kinds of quantitative pharmacophoric models with ILP: (a) Models that predict the probability that a ligand is “active”; and (b) Models that predict the actual medicinal activity of a ligand. Quantitative predictions are obtained by the utilising the following statistical procedures as background knowledge: logistic regression and naive Bayes, for probability prediction; linear and kernel regression, for activity prediction. The multi-conformation issue and, more generally, the relational representation used by ILP results in some special difficulties in the use of any statistical procedure. We present the principal issues and some solutions. Specifically, using data on the inhibition of the protease Thermolysin, we demonstrate that it is possible for an ILP program to construct good quantitative structure-activity models. We also comment on the relationship of this work to other recent developments in statistical relational learning. Editors: Tamás Horváth and Akihiro Yamamoto     

A Relational Model of Workplace Victimization: Social Roles and Patterns of Victimization in Dyadic Relationships.

This article proposes a model of the ways in which dyadic interactions between employees who occupy 1 of 4 archetypal social roles in organizations can lead to either episodic or institutionalized patterns of victimization. The model shows how the occurrence of victimization involving these 4 role types is influenced by organizational variables such as power differences, culture, and access to social capital. The model integrates behavioral and social structural antecedents of victimization to develop a relational perspective on the dynamics of harmful behavior in the workplace. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A survey of parallel execution strategies for transitive closure and logic programs

An important feature of database technology of the nineties is the use of parallelism for speeding up the execution of complex queries. This technology is being tested in several experimental database architectures and a few commercial systems for conventional select-project-join queries. In particular, hash-based fragmentation is used to distribute data to disks under the control of different processors in order to perform selections and joins in parallel. With the development of new query languages, and in particular with the definition of transitive closure queries and of more general logic programming queries, the new dimension of recursion has been added to query processing. Recursive queries are complex; at the same time, their regular structure is particularly suited for parallel execution, and parallelism may give a high efficiency gain. We survey the approaches to parallel execution of recursive queries that have been presented in the recent literature. We observe that research on parallel execution of recursive queries is separated into two distinct subareas, one focused on the transitive closure of Relational Algebra expressions, the other one focused on optimization of more general Datalog queries. Though the subareas seem radically different because of the approach and formalism used, they have many common features. This is not surprising, because most typical Datalog queries can be solved by means of the transitive closure of simple algebraic expressions. We first analyze the relationship between the transitive closure of expressions in Relational Algebra and Datalog programs. We then review sequential methods for evaluating transitive closure, distinguishing iterative and direct methods. We address the parallelization of these methods, by discussing various forms of parallelization. Data fragmentation plays an important role in obtaining parallel execution; we describe hash-based and semantic fragmentation. Finally, we consider Datalog queries, and present general methods for parallel rule execution; we recognize the similarities between these methods and the methods reviewed previously, when the former are applied to linear Datalog queries. We also provide a quantitative analysis that shows the impact of the initial data distribution on the performance of methods. Recommended by: Patrick Valduriez     

A semantic modeling approach for image retrieval by content

We introduce a semantic data model to capture the hierarchical, spatial, temporal, and evolutionary semantics of images in pictorial databases. This model mimics the user's conceptual view of the image content, providing the framework and guidelines for preprocessing to extract image features. Based on the model constructs, a spatial evolutionary query language (SEQL), which provides direct image object manipulation capabilities, is presented. With semantic information captured in the model, spatial evolutionary queries are answered efficiently. Using an object-oriented platform, a prototype medical-image management system was implemented at UCLA to demonstrate the feasibility of the proposed approach.     

Object-oriented DBMS requirements

The requirements on an object-oriented DBMS for management of information in a large, complex enterprise are presented. These requirements aid in the achievement of an environment characterized by data sharing, open architectures, application and data portability, and assurance of data integrity. They were defined from the point of view of a user of the DBMS; therefore they describe the expected functionality of the DBMS and do not specify the method of implementation to achieve this functionality. They encompass requirements on the data model, query and data manipulation languages, the system architecure, interfaces to the system, change management, and transaction management.     

Contextualizing is not nullifying: Reply to Mills (2005).

In omitting crucial words and sentencees, neglecting relevant citations, and overlooking important distinctions, Jon Mills' (see record 2005-04819-001) critique of relational psychoanalysis significantly misrepresents the authors' viewpoint. This viewpoint seeks to contextualize, but not to nullify, individual worlds of experience and their limiting horizons. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Object data MODEL = object-oriented + semantic models

The term ‘object-oriented database’ has been used to refer to different characteristics and mechanisms supported by semantic databases and (behaviorally) object-oriented ones. While this indicates the current confusion due to the lack of a common model, it also suggests the potential desirability of combining these two kinds of modeling facilities into the same nutshell. This paper summarizes from these two paradigms the features common to both, the features influenced/adopted by each other, and the features which are presented in one paradigm but missing from the other. After a brief analysis and discussion of these features, we conclude this paper by proposing our major theme: a complete object data model should take the union of the facilities offered by these two kinds of models.     

HiSQL: A Front-end Query System for Historical Relational Databases

The paper describes a prototype system called HiSQL (Historical SQL) which extends the functionality of SQL in manipulating historical data, by providing functions for spatial and temporal processing. Conceptually the paper is divided into three parts: the first part deals with the design and architecture of the system; the second part introduces a case study (the defters); and the third part describes specific functions for spatial and temporal processing of serial documents. The paper concludes with a comparison between HiSQL and SQL and suggestions for further work. This revised version was published online in August 2006 with corrections to the Cover Date.     

SQL语言中量词和空值的使用技术

在ＳＱＬ语言中可以引入全称量词符号ＦＯＲＡＬＬ，使ＳＱＬ语言使用更为自然，方便。本文讨论全称量词，存在量词和ＡＬＬ三种谓词之间的转换，联系和区别，以及空值存在时ＳＱＬ的使用技术。