Lightweight String Reasoning for OCL

International audienceModels play a key role in assuring software quality in the modeldriven approach. Precise models usually require the definition of OCL expressions to specify model constraints that cannot be expressed graphically. Techniques that check the satisfiability of such models and find corresponding instances of them are important in various activities, such as model-based testing and validation. Several tools to check model satisfiability have been developed but to our knowledge, none of them yet supports the analysis of OCL expressions including operations on Strings in general terms. As, in contrast, many industrial models do contain such operations, there is evidently a gap. There has been much research on formal reasoning on strings in general, but so far the results could not be included into model finding approaches. For model finding, string reasoning only contributes a sub-problem, therefore, a string reasoning approach for model finding should not add up front too much computational complexity to the global model finding problem. We present such a lightweight approach based on constraint satisfaction problems and constraint rewriting. Our approach efficiently solves several common kinds of string constraints and it is integrated into the EMFtoCSP model finder

Systematic identification of conserved motif modules in the human genome

<p>Abstract</p> <p>Background</p> <p>The identification of motif modules, groups of multiple motifs frequently occurring in DNA sequences, is one of the most important tasks necessary for annotating the human genome. Current approaches to identifying motif modules are often restricted to searches within promoter regions or rely on multiple genome alignments. However, the promoter regions only account for a limited number of locations where transcription factor binding sites can occur, and multiple genome alignments often cannot align binding sites with their true counterparts because of the short and degenerative nature of these transcription factor binding sites.</p> <p>Results</p> <p>To identify motif modules systematically, we developed a computational method for the entire non-coding regions around human genes that does not rely upon the use of multiple genome alignments. First, we selected orthologous DNA blocks approximately 1-kilobase in length based on discontiguous sequence similarity. Next, we scanned the conserved segments in these blocks using known motifs in the TRANSFAC database. Finally, a frequent pattern mining technique was applied to identify motif modules within these blocks. In total, with a false discovery rate cutoff of 0.05, we predicted 3,161,839 motif modules, 90.8% of which are supported by various forms of functional evidence. Compared with experimental data from 14 ChIP-seq experiments, on average, our methods predicted 69.6% of the ChIP-seq peaks with TFBSs of multiple TFs. Our findings also show that many motif modules have distance preference and order preference among the motifs, which further supports the functionality of these predictions.</p> <p>Conclusions</p> <p>Our work provides a large-scale prediction of motif modules in mammals, which will facilitate the understanding of gene regulation in a systematic way.</p

High-Order SNP Combinations Associated with Complex Diseases: Efficient Discovery, Statistical Power and Functional Interactions

There has been increased interest in discovering combinations of single-nucleotide polymorphisms (SNPs) that are strongly associated with a phenotype even if each SNP has little individual effect. Efficient approaches have been proposed for searching two-locus combinations from genome-wide datasets. However, for high-order combinations, existing methods either adopt a brute-force search which only handles a small number of SNPs (up to few hundreds), or use heuristic search that may miss informative combinations. In addition, existing approaches lack statistical power because of the use of statistics with high degrees-of-freedom and the huge number of hypotheses tested during combinatorial search. Due to these challenges, functional interactions in high-order combinations have not been systematically explored. We leverage discriminative-pattern-mining algorithms from the data-mining community to search for high-order combinations in case-control datasets. The substantially improved efficiency and scalability demonstrated on synthetic and real datasets with several thousands of SNPs allows the study of several important mathematical and statistical properties of SNP combinations with order as high as eleven. We further explore functional interactions in high-order combinations and reveal a general connection between the increase in discriminative power of a combination over its subsets and the functional coherence among the genes comprising the combination, supported by multiple datasets. Finally, we study several significant high-order combinations discovered from a lung-cancer dataset and a kidney-transplant-rejection dataset in detail to provide novel insights on the complex diseases. Interestingly, many of these associations involve combinations of common variations that occur in small fractions of population. Thus, our approach is an alternative methodology for exploring the genetics of rare diseases for which the current focus is on individually rare variations

On the local closedworld assumption of data-sources

Abstract. The Closed-World Assumption (CWA) on a database ex-presses that an atom not in the database is false. The CWA is only applicable in domains where the database has complete knowledge. In many cases, for example in the context of distributed databases, a data source has only complete knowledge about part of the domain of dis-course. In this paper, we introduce an expressive and intuitively appeal-ing method of representing a local closed-world assumption (LCWA) of autonomous data-sources. This approach distinguishes between the data that is conveyed by a data-source and the meta-knowledge about the area in which these data is complete. The data is stored in a relational database that can be queried in the standard way, whereas the meta-knowledge about its completeness is expressed by a first order theory that can be processed by an independent reasoning system (for example a mediator). We consider different ways of representing our approach, relate it to other methods of representing local closed-word assumptions of data-sources, and show some useful properties of our framework which facilitate its application in real-life systems.

Pushing tougher constraints in frequent pattern mining

Abstract. In this paper we extend the state-of-art of the constraints that can be pushed in a frequent pattern computation. We introduce a new class of tough constraints, namely Loose Anti-monotone constraints, and we deeply characterize them by showing that they are a superclass of convertible anti-monotone constraints (e.g. constraints on average or median) and that they model tougher constraints (e.g. constraints on variance or standard deviation). Then we show how these constraints can be exploited in a level-wise Apriori-like computation by means of a new data-reduction technique: the resulting algorithm outperforms previous proposals for convertible constraints, and it is to treat much tougher constraints with the same effectiveness of easier ones.