Abstract
It has been recognized that the development of new therapeutic drugs is a complex and expensive process. A large number of factors affect the activity in vivo of putative candidate molecules and the propensity for causing adverse and toxic effects is recognized as one of the major hurdles behind the current "target-rich, lead-poor" scenario. Structure-Activity Relationship (SAR) studies, using relational Machine Learning (ML) algorithms, have already been shown to be very useful in the complex process of rational drug design. Despite the ML successes, human expertise is still of the utmost importance in the drug development process. An iterative process and tight integration between the models developed by ML algorithms and the know-how of medicinal chemistry experts would be a very useful symbiotic approach. In this paper we describe a software tool that achieves that goal--iLogCHEM. The tool allows the use of Relational Learners in the task of identifying molecules or molecular fragments with potential to produce toxic effects, and thus help in stream-lining drug design in silico. It also allows the expert to guide the search for useful molecules without the need to know the details of the algorithms used. The models produced by the algorithms may be visualized using a graphical interface, that is of common use amongst researchers in structural biology and medicinal chemistry. The graphical interface enables the expert to provide feedback to the learning system. The developed tool has also facilities to handle the similarity bias typical of large chemical databases. For that purpose the user can filter out similar compounds when assembling a data set. Additionally, we propose ways of providing background knowledge for Relational Learners using the results of Graph Mining algorithms. Copyright 2011 The Author(s). Published by Journal of Integrative Bioinformatics.

Abstract
The WaveScalar is the first DataFlow Architecture that can efficiently provide the sequential memory semantics required by imperative languages. This work presents a speculative memory disambiguation mechanism for this architecture, the Transaction WaveCache. Our mechanism maintains the execution order of memory operations within blocks of code, called Waves, but adds the ability to speculatively execute, our-of-order operations front different waves. This mechanism is inspired by progress in supporting Transactional Memories. Waves are considered as atomic regions and executed as nested transactions. Wave that have finished the execution of all their memory operations are committed, as soon as the previous waves are also committed. If a hazard is detected in a speculative Wave, all the following Waves (children) are aborted and re-executed. We evaluated the Transactional WaveCache oil a set of benchmarks from Spec 2000, Mediabench and Mibench (telecomm). Speedups ranging from 1.31 to 2.24 (related to the original WaveScalar) where observed when the benchmark doesn't perform lots of emulated function calls or access memory very often. Low speedups of 1.1 to slowdowns of 0.96 were observed when the opposite happens or when the memory concurrency was high.

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(Non-)portability of Prolog programs is widely considered as an important factor in the lack of acceptance of the language. Since 1995, the core of the language is covered by the ISO standard 13211-1. Since 2007, YAP and SWI-Prolog have established a basic compatibility framework. This article describes and evaluates this framework. The aim of the framework is running the same code on both systems rather than migrating an application. We show that today, the portability within the family of Edinburgh/Quintus derived Prolog implementations is good enough to allow for maintaining portable real-world applications.

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