Recursive Database Research Articles

Multi-DOF compensation of piezoelectric actuators with recursive databases

Abstract Piezoelectric actuators are subject to nonlinear effects when voltage-driven in open-loop control. In particular, hysteresis and creep effects are dominating nonlinearities that significantly deteriorate performance in tracking control scenarios. In this paper, we present an online compensator suitable for piezoelectric actuators that is based on the modified Prandtl-Ishlinskii model and utilizes recursive databases for the compensation of nonlinearities. The compensator scheme is furthermore extended to systems with more than one degree of freedom (DOF) such as Cartesian manipulators by employing a decoupling control design to mitigate inherent cross-coupling disturbances. In order to validate our theoretical derivations, experiments are conducted with coupled trajectories on a commercial 3-DOF micro-positioning unit driven by piezoelectric actuators.

Tracembler – software for in-silico chromosome walking in unassembled genomes

BackgroundWhole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user.ResultsTracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus.ConclusionTracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at , and the software is also freely available from the authors for local installations.

Recursive database structures

Recursion has always been an interesting topic in computer science, and one of the most difficult data structures to implement in modern relational database systems is recursive relationships. In a...

On computing minimal and perfect model membership

The computational complexity of a number of problems relating to minimal models of non-Horn deductive databases is considered. In particular, the problem of determining minimal model membership is shown to be NP-complete for non recursive propositional databases. The structure of minimal models is also examined using the notion of a cyclic tree, and methods of determining minimal model membership, minimality of models and compiling the GCWA are presented. The handling of negative premises is also considered using perfect model semantics, and methods for computing perfect model membership are presented.

RQL: a recursive query language

Different classes of recursive queries in the relational databases are identified. It is shown that existing proposals to extend the relational query languages are either not powerful enough to express queries in many of these classes or use nonfirst normal form constructs. RQL, a recursive database query language that can be used to express recursive queries on all the classes identified, is presented. RQL is based on the relational algebra. In addition to functions that correspond to the standard and extended relational algebra operators, RQL supports functions required to express general recursive queries. The elements of RQL and the ways in which they are used to formulate complicated, but useful, recursive queries are described. The effects of the extensions embodied in RQL on the termination of recursive query evaluation are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

A simple characterization of uniform boundedness for a class of recursions

Detecting bounded recursions is a powerful optimization technique for recursive database query languages, as bounded recursions can be replaced by equivalent nonrecursive definitions. The problem is also of theoretical interest in that varying the class of recursions considered generates problem instances that vary from linearly decidable to NP-hard to undecidable. In this paper we review and clarify the existing definitions of boundedness. We then specify a class of recursions C such that membership in C guarantees that a certain simple condition is necessary and sufficient for boundedness. We use the notion of membership in C to unify and extend previous work on determining decidable classes of bounded recursions.

Query evaluation in recursive databases: bottom-up and top-down reconciled

It is desirable to answer queries posed to deductive databases by computing fixpoints because such computations are directly amenable to set-oriented fact processing. However, the classical fixpoint procedures based on bottom-up processing — the naive and semi-naive methods — are rather primitive and often inefficient. In this article, we rely on bottom-up meta-interpretation for formalizing a new fixpoint procedure that performs a different kind of reasoning: We specify a top-down query answering method, which we call the Backward Fixpoint Procedure. Then, we reconsider query evaluation methods for recursive databases. First, we show that the methods based on rewriting on the one hand, and the methods based on resolution on the other hand, implement the Backward Fixpoint Procedure. Second, we interpret the rewritings of the Alexander and Magic Set methods as specializations of the Backward Fixpoint Procedure. Finally, we argue that such a rewriting is also needed in a database context for implementing efficiently the resolution-based methods. Thus, the methods based on rewriting and the methods based on resolution implement the same top-down evaluation of the original database rules by means of auxiliary rules processed bottom-up.

A two-path recursive relational database structure for molecular information systems

A recursive relational database structure, called the two-path structure, is proposed for holding data about the properties and structure of molecules. The two-path database approach solves certain severe restriction problems by providing two pathways to the structure of complex chemical entities. One pathway permits a fast descent to the atomic structure in terms of correct IUPAC carbon atom occurrence numbers. The other pathway descends through the molecular substructures, which can be referenced at any level in retrievals. The database appears to be capable of faithfully recording the structure of all chemical entities, including proteins and enzymes.

An approach to the recursive retrieval problem in the relational database

The host query language often impairs data retrieval in recursive database structures. Functional extensions to QUEL are explored in order to simplify the user interface.

Algebraic Optimization Of Recursive Database Queries

AbstractThe topic is algebraic optimization of recursive database queries. Queries are expressed by relational algebra expressions including a fixpoint operation. A condition is presented under which a natural join commutes with a fixpoint operation. This condition is a simple check of attribute sets of sub-expressions of the query. The work may be considered a generalization of Aho and Ullman, (1979).The result is interpreted in function free logic database terms as a transformation of the recursively defined predicate involving: (a) elimination of an argument, and (b) propagation of selections (instantiations) to the extensionally defined predicates. A collection of examples shows that this transformation abstracts some optimizations which otherwise are done by more complex graph algorithms (e.g. Bancilhon et al., (1986); Chang, (1985); Gardarin and DeMaindreville, (1986); Henschen and Naqvi, (1984); Kifer and Lozinskii, (1986)). Thus, this optimization is expressed in a form which is not biased towards...

Handling redundancy in the processing of recursive database queries

Redundancy may exist in the processing of recursive database queries at four different levels precompilation level, iteration level, tuple processing level and file accessing level. Techniques for reducing redundant work at each level are studied. In the precompilation level, the optimization techniques include removing redundant parts in a rule cluster, simplifying recursive clusters and sharing common subexpressions among rules. At the iteration level, the techniques discussed are the use of frontier relations and the counting method. At the tuple processing level, we use merging and filtering methods to exclude processed drivers from database reaccessing. Finally, at the file accessing level, I/O cost can be further reduced by level relaxation. We conclude that even for complex recursion, redundant database processing can be considerably reduced or eliminated by developing appropriate algorithms.