Finding Anchors for Genomic Sequence Comparison

title: Finding anchors for genomic sequence comparison
abstract: Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole genomes generally use a seed-and-extend technique, starting from exact or near-exact matches and selecting a reliable subset of these, called anchors, and then filling in the remaining portions between the anchors using a combination of local and global alignment algorithms, but their choices for the parameters so far have been primarily heuristic. We present a statistical framework and practical methods for selecting a set of matches that is both sensitive and specific and can constitute a reliable set of anchors for a one-to-one mapping of two genomes from which a whole-genome alignment can be built. Starting from exact matches, we introduce a novel per-base repeat annotation, the $Z$-score, from which noise and repeat filtering conditions are explored. Dynamic programming-based chaining algorithms are also evaluated as context-based filters. We apply the methods described here to the comparison of two progressive assemblies of the human genome, NCBI build 28 and build 34 http://genome.ucsc.edu), and show that a significant portion of the two genomes can be found in selected exact matches, with very limited amount of sequence duplication.

title: An approach to hardware/software partitioning for multiple hardware devices model
abstract: Computer aided hardware/software partitioning is one of the key challenges in hardware/software co-design. This paper describes a new approach to hardware/software partitioning for multiple hardware-devices model. The partitioning is transformed into a reachability problem of timed automata, and the optimal solution can be obtained by means of an optimal reachability algorithm. To relax the initial condition of partitioning for optimization, two algorithms are designed to explore the dependency relations among processes in the sequential specification. Some experiments are conducted with model checker UPPAAL to show our approach is both effective and efficient.

title: Some Algorithms for Extension Computation of Nonmonotonic Rule Systems
abstract: In this paper, we will place our emphasis on the problem of existence of extensions and on finding more efficient algorithms for computing extensions of nonmonotonic rule systems. First, in order to dedicate further research into nonmonotonic rule systems a new characterization and some new results are given. This characterization and these results lead to new algorithms for computing extensions. Second, a class of nonmonotonic rule systems, called regular nonmonotonic rule systems, is developed. The existence of extensions and semi-monotonicity of regular nonmonotonic rule systems are proved. Third, we prove that each regular nonmonotonic rule system has at most 1.47^n extensions, where n is the number of elements occurring in the system.

title: Semantics of BPEL4WS-Like Fault and Compensation Handling
abstract: BPEL4WS is one of the most important business process modelling languages. One distinct feature of it is the fully programmable fault and compensation handling mechanism, which allows the user to specify the compensation behaviors of processes in application-specific manners. In this paper, we present a formal operational semantics to a simplified version of BPEL4WS, with some important concepts related to fault and compensation handling proposed and discussed, especially, the compensation closure and the compensation context. We also discuss some insights into the BPEL4WS language and its implementation obtained from this study.

title: Quantifier Rewriting and Equivalence Models for Quantified Horn Formulas
abstract: In this paper, quantified Horn formulas with free variables (QHORN*) are investigated. The main result is that any quantified Horn formula Φ of length |Φ| with free variables, |∀| universal quantifiers and an arbitrary number of existential quantifiers can be transformed into an equivalent formula of length O(|∀| ·|Φ|) which contains only existential quantifiers. Moreover, it is shown that quantified Horn formulas with free variables have equivalence models where every existential quantifier is associated with a monotone Boolean function. 
 
The results allow a simple representation of quantified Horn formulas as purely existentially quantified Horn formulas . An application described in the paper is to solve QHORN*-SAT in O(|∀| ·|Φ|) by using this transformation in combination with a linear-time satisfiability checker for propositional Horn formulas.

title: Siren: catching evasive malware
abstract: With the growing popularity of anomaly detection systems, which is due partly to the rise in zero-day attacks, a new class of threats have evolved where the attacker mimics legitimate activity to blend in and avoid detection. We propose a new system called Siren that injects crafted human input alongside legitimate user activity to thwart these mimicry attacks. The crafted input is specially designed to trigger a known sequence of network requests, which Siren compares to the actual traffic. It then flags unexpected messages as malicious. Using this method, we were able to detect ten spyware programs that we tested, many of which attempt to blend in with user activity. This paper presents the design, implementation, and evaluation of the Siren activity injection system, as well as a discussion of its potential limitations