Abstract
Determining the underlying regulatory mechanism of genetic networks is one of the central challenges of computational biology. Numerous methods have been developed and applied to the important but complex task of reverse engineering regulatory networks from high-throughput gene expression data. However, many challenges remain. In this paper, we are interested in learning rules that will reveal the causal genes for the expression variation from various relational data sources in addition to gene expression data. Following our previous work where we showed that time series gene expression data could potentially uncover causal effects, we describe an application of an inductive logic programming (ILP) system, to the task of identifying important regulatory relationships from discretized time series gene expression data, protein-protein interaction, protein phosphorylation and transcription factor data about the organism. Specifically, we learn rules for predicting gene expression levels at the next time step based on the available relational data and then generalize the learned theory to visualize a pruned network of important interactions. We evaluate and present experimental results on microarray experiments from Gasch et al on Saccharomyces cerevisiae.

Abstract
As logic programming applications grow in size, Prolog systems need to efficiently access larger and larger data sets and the need for any- and multi-argument indexing becomes more and more profound. Static generation of multi-argument indexing is one alternative, but applications often rely on features that are inherently dynamic which makes static techniques inapplicable or inaccurate. Another alternative is to employ dynamic schemes for flexible demand-driven indexing of Prolog clauses. We propose such schemes and discuss issues that need to be addressed for their efficient implementation in the context of WAM-based Prolog systems. We have implemented demand-driven indexing in two different Prolog systems and have been able to obtain non-negligible performance speedups: from a few percent up to orders of magnitude. Given these results, we see very little reason for Prolog systems not to incorporate some form of dynamic indexing based on actual demand. In fact, we see demand-driven indexing as only the first step towards effective runtime optimization of Prolog programs.

Abstract
The development of large mammography databases provides an opportunity for knowledge discovery and data mining techniques to recognize patterns not previously appreciated. Using a database from a breast imaging practice containing patient risk factors, imaging findings, and biopsy results, we tested whether inductive logic programming (ILP) could discover interesting hypotheses that could subsequently be tested and validated. The ILP algorithm discovered two hypotheses from the data that were 1) judged as interesting by a subspecialty trained mammographer and 2) validated by analysis of the data itself.

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.

Abstract