P Systems with Minimal Left and Right Insertion and Deletion

In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol

P Systems with Minimal Left and Right Insertion and Deletion

Summary. In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol.

Identifying Causal Effects via Context-specific Independence Relations

Peer reviewe

Computational Complexity And Algorithms For Dirty Data Evaluation And Repairing

In this dissertation, we study the dirty data evaluation and repairing problem in relational database. Dirty data is usually inconsistent, inaccurate, incomplete and stale. Existing methods and theories of consistency describe using integrity constraints, such as data dependencies. However, integrity constraints are good at detection but not at evaluating the degree of data inconsistency and cannot guide the data repairing. This dissertation first studies the computational complexity of and algorithms for the database inconsistency evaluation. We define and use the minimum tuple deletion to evaluate the database inconsistency. For such minimum tuple deletion problem, we study the relationship between the size of rule set and its computational complexity. We show that the minimum tuple deletion problem is NP-hard to approximate the minimum tuple deletion within 17/16 if given three functional dependencies and four attributes involved. A near optimal approximated algorithm for computing the minimum tuple deletion is proposed with a ratio of 2 − 1/2r , where r is the number of given functional dependencies. To guide the data repairing, this dissertation also investigates the data repairing method by using query feedbacks, formally studies two decision problems, functional dependency restricted deletion and insertion propagation problem, corresponding to the feedbacks of deletion and insertion. A comprehensive analysis on both combined and data complexity of the cases is provided by considering different relational operators and feedback types. We have identified the intractable and tractable cases to picture the complexity hierarchy of these problems, and provided the efficient algorithm on these tractable cases. Two improvements are proposed, one focuses on figuring out the minimum vertex cover in conflict graph to improve the upper bound of tuple deletion problem, and the other one is a better dichotomy for deletion and insertion propagation problems at the absence of functional dependencies from the point of respectively considering data, combined and parameterized complexities

Causal Effect Identification from Multiple Incomplete Data Sources: A General Search-Based Approach

Peer reviewe

Formal models of the extension activity of DNA polymerase enzymes

The study of formal language operations inspired by enzymatic actions on DNA is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion-deletion systems, substitution, hairpin extension, hairpin reduction, superposition, overlapping concatenation, conditional concatenation, contextual intra- and intermolecular recombinations, as well as template-guided recombination. First, a formal language operation is proposed and investigated, inspired by the naturally occurring phenomenon of DNA primer extension by a DNA-template-directed DNA polymerase enzyme. Given two DNA strings u and v, where the shorter string v (called the primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called the template) the result of the primer extension is a DNA string that is complementary to a suffix of the template which starts at the binding position of the primer. The operation of DNA primer extension can be abstracted as a binary operation on two formal languages: a template language L1 and a primer language L2. This language operation is called L1-directed extension of L2 and the closure properties of various language classes, including the classes in the Chomsky hierarchy, are studied under directed extension. Furthermore, the question of finding necessary and sufficient conditions for a given language of target strings to be generated from a given template language when the primer language is unknown is answered. The canonic inverse of directed extension is used in order to obtain the optimal solution (the minimal primer language) to this question. The second research project investigates properties of the binary string and language operation overlap assembly as defined by Csuhaj-Varju, Petre and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an overlap y, results in the string xyz. In this context, we investigate overlap assembly and its properties: closure properties of various language families under this operation, and related decision problems. A theoretical analysis of the possible use of iterated overlap assembly to generate combinatorial DNA libraries is also given. The third research project continues the exploration of the properties of the overlap assembly operation by investigating closure properties of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. The problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two other given languages are also investigated