A New Lower Bound on the Maximum Number of Satisfied Clauses in Max-SAT and its Algorithmic Applications

A pair of unit clauses is called conflicting if it is of the form $(x)$, $(\bar{x})$. A CNF formula is unit-conflict free (UCF) if it contains no pair of conflicting unit clauses. Lieberherr and Specker (J. ACM 28, 1981) showed that for each UCF CNF formula with $m$ clauses we can simultaneously satisfy at least \pp m clauses, where \pp =(\sqrt{5}-1)/2. We improve the Lieberherr-Specker bound by showing that for each UCF CNF formula $F$ with $m$ clauses we can find, in polynomial time, a subformula $F'$ with $m'$ clauses such that we can simultaneously satisfy at least \pp m+(1-\pp)m'+(2-3\pp)n"/2 clauses (in $F$), where $n"$ is the number of variables in $F$ which are not in $F'$. We consider two parameterized versions of MAX-SAT, where the parameter is the number of satisfied clauses above the bounds $m/2$ and $m(\sqrt{5}-1)/2$. The former bound is tight for general formulas, and the later is tight for UCF formulas. Mahajan and Raman (J. Algorithms 31, 1999) showed that every instance of the first parameterized problem can be transformed, in polynomial time, into an equivalent one with at most $6k+3$ variables and $10k$ clauses. We improve this to $4k$ variables and $(2\sqrt{5}+4)k$ clauses. Mahajan and Raman conjectured that the second parameterized problem is fixed-parameter tractable (FPT). We show that the problem is indeed FPT by describing a polynomial-time algorithm that transforms any problem instance into an equivalent one with at most $(7+3\sqrt{5})k$ variables. Our results are obtained using our improvement of the Lieberherr-Specker bound above

Scrap your boilerplate with object algebras

htmlabstractTraversing complex Abstract Syntax Trees (ASTs) typically requires large amounts of tedious boilerplate code. For many operations most of the code simply walks the structure, and only a small portion of the code implements the functional- ity that motivated the traversal in the first place. This paper presents a type-safe Java framework called Shy that removes much of this boilerplate code. In Shy Object Algebras are used to describe complex and extensible AST structures. Using Java annotations Shy generates generic boilerplate code for various types of traversals. For a concrete traversal, users of Shy can then inherit from the generated code and over- ride only the interesting cases. Consequently, the amount of code that users need to write is significantly smaller. Moreover, traversals using the Shy framework are also much more structure shy, becoming more adaptive to future changes or extensions to the AST structure. To prove the effectiveness of the approach, we applied Shy in the implementation of a domain-specific questionnaire language. Our results show that for a large number of traversals there was a significant reduction in the amount of user-defined code

Understanding Design Patterns Density with Aspects: A Case Study in JHotDraw using AspectJ

International audienceDesign patterns offer solutions to common engineering prob- lems in programs [1]. In particular, they shape the evolution of program elements. However, their implementations tend to vanish in the code: thus it is hard to spot them and to understand their impact. The prob- lem becomes even more difficult with a "high density of pattern": then the program becomes easy to evolve in the direction allowed by patterns but hard to change [2]. Aspect languages offer new means to modular- ize elements. Implementations of object-oriented design patterns with AspectJ have been proposed [3]. We aim at testing the scalability of such solutions in the JHotDraw framework. We first explore the impact of density on pattern implementation. We show how AspectJ helps to reduce this impact. This unveils the principles of aspects and AspectJ to control pattern density

Synthesizing Iterators from Abstraction Functions

A technique for synthesizing iterators from declarative abstraction functions written in a relational logic specification language is described. The logic includes a transitive closure operator that makes it convenient for expressing reachability queries on linked data structures. Some optimizations, including tuple elimination, iterator flattening, and traversal state reduction, are used to improve performance of the generated iterators. A case study demonstrates that most of the iterators in the widely used JDK Collections classes can be replaced with code synthesized from declarative abstraction functions. These synthesized iterators perform competitively with the hand-written originals. In a user study the synthesized iterators always passed more test cases than the hand-written ones, were almost always as efficient, usually took less programmer effort, and were the qualitative preference of all participants who provided free-form comments

Scrap your boilerplate with object algebras

International audienceTraversing complex Abstract Syntax Trees (ASTs) typically requires large amounts of tedious boilerplate code. For many operations most of the code simply walks the structure, and only a small portion of the code implements the functional- ity that motivated the traversal in the first place. This paper presents a type-safe Java framework called Shy that removes much of this boilerplate code. In Shy Object Algebras are used to describe complex and extensible AST structures. Using Java annotations Shy generates generic boilerplate code for various types of traversals. For a concrete traversal, users of Shy can then inherit from the generated code and over- ride only the interesting cases. Consequently, the amount of code that users need to write is significantly smaller. Moreover, traversals using the Shy framework are also much more structure shy, becoming more adaptive to future changes or extensions to the AST structure. To prove the effectiveness of the approach, we applied Shy in the implementation of a domain-specific questionnaire language. Our results show that for a large number of traversals there was a significant reduction in the amount of user-defined code

Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields

We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constraints for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

The Regulation of MS-KIF18A Expression and Cross Talk with Estrogen Receptor

This study provides a novel view on the interactions between the MS-KIF18A, a kinesin protein, and estrogen receptor alpha (ERα) which were studied in vivo and in vitro. Additionally, the regulation of MS-KIF18A expression by estrogen was investigated at the gene and protein levels. An association between recombinant proteins; ERα and MS-KIF18A was demonstrated in vitro in a pull down assay. Such interactions were proven also for endogenous proteins in MBA-15 cells were detected prominently in the cytoplasm and are up-regulated by estrogen. Additionally, an association between these proteins and the transcription factor NF-κB was identified. MS-KIF18A mRNA expression was measured in vivo in relation to age and estrogen level in mice and rats models. A decrease in MS-KIF18A mRNA level was measured in old and in OVX-estrogen depleted rats as compared to young animals. The low MS-KIF18A mRNA expression in OVX rats was restored by estrogen treatment. We studied the regulation of MS-KIF18A transcription by estrogen using the luciferase reporter gene and chromatin immuno-percipitation (ChIP) assays. The luciferase reporter gene assay demonstrated an increase in MS-KIF18A promoter activity in response to 10−8 M estrogen and 10−7M ICI-182,780. Complimentary, the ChIP assay quantified the binding of ERα and pcJun to the MS-KIF18A promoter that was enhanced in cells treated by estrogen and ICI-182,780. In addition, cells treated by estrogen expressed higher levels of MS-KIF18A mRNA and protein and the protein turnover in MBA-15 cells was accelerated. Presented data demonstrated that ERα is a defined cargo of MS-KIF18A and added novel insight on the role of estrogen in regulation of MS-KIF18A expression both in vivo and in vitro