Updates and Subjunctive Queries

AbstractA subjunctive query of the form φ > ψ, means "if φ were true in the knowledgebase, would ψ also necessarily be true?" We propose the following semantics for subjunctive queries: φ > ψ, will hold in the current knowledgebase T if ψ holds in the result of updating T with φ. This is known as the Ramsey test in philosophy. We adapt the model checking approach of Halpern and Vardi: A knowledgebase is a finite set of finite sets of positive facts interpreted in a closed world setting. We then use Winslett′s possible models approach to give semantics to knowledgebase updates, and we introduce a query language which is essentially propositional logic, augmented with a subjunctive conditional that has an intensional interpretation in our model. We show that query answering and update can be performed in time polynomial in the size of the knowledgebase. However, query equivalence is shown to be complete in polynomial space, and this is also the complexity of query answering as a function of query size. We give a sound axiomatization of query equivalence and show that the update operator satisfies the postulates for updates adapted by Katsuno and Mendelzon from the Alchourrón-Gärdenfors-Makinson belief revision postulates

Children's game library as a Unique Extracurricular Educational Establishment in the USSR (the middle of the 20th century)

The article reveals the history of emergence and work of children's game libraries in the USSR in the middle of the 20th century. The first children's game libraries, which were educational establishments where children could come and play different games, using various game and sport equipment free of charge, appeared in the 1930th and became wide spread in the USSR in the 1930th - 1950th. Children's game libraries had different tasks of their work (organizing children's cultural leisure time, increasing the educational and political levels of children's games and entertainments which were conducted in schools, summer camps and extracurricular educational establishments). They also had different directions of their work, namely: organizational, methodic, educational, experimental, instructive and consultative directions. It has been shown in the article that children’s game libraries had great results of their work (they involved a lot of children and adults in their activities; the network of children's game libraries began to grow; a lot of new toys and games were created and produced by them). However, children's game libraries faced certain difficulties in their work, namely: absence of own premises of children’s game libraries, lack of enough support for their activities by some educational institutions and teaching staff, lack of the required amount of toys and games, insufficient instructive and publishing activities of children’s game libraries

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