Dynamic Ordered Sets with Exponential Search Trees

We introduce exponential search trees as a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. This leads to an optimal bound of O(sqrt(log n/loglog n)) for searching and updating a dynamic set of n integer keys in linear space. Here searching an integer y means finding the maximum key in the set which is smaller than or equal to y. This problem is equivalent to the standard text book problem of maintaining an ordered set (see, e.g., Cormen, Leiserson, Rivest, and Stein: Introduction to Algorithms, 2nd ed., MIT Press, 2001). The best previous deterministic linear space bound was O(log n/loglog n) due Fredman and Willard from STOC 1990. No better deterministic search bound was known using polynomial space. We also get the following worst-case linear space trade-offs between the number n, the word length w, and the maximal key U < 2^w: O(min{loglog n+log n/log w, (loglog n)(loglog U)/(logloglog U)}). These trade-offs are, however, not likely to be optimal. Our results are generalized to finger searching and string searching, providing optimal results for both in terms of n.Comment: Revision corrects some typoes and state things better for applications in subsequent paper

Model Creation and Equivalence Proofs of Cellular Automata and Artificial Neural Networks

Computational methods and mathematical models have invaded arguably every scientific discipline forming its own field of research called computational science. Mathematical models are the theoretical foundation of computational science. Since Newton's time, differential equations in mathematical models have been widely and successfully used to describe the macroscopic or global behaviour of systems. With spatially inhomogeneous, time-varying, local element-specific, and often non-linear interactions, the dynamics of complex systems is in contrast more efficiently described by local rules and thus in an algorithmic and local or microscopic manner. The theory of mathematical modelling taking into account these characteristics of complex systems has to be established still. We recently presented a so-called allagmatic method including a system metamodel to provide a framework for describing, modelling, simulating, and interpreting complex systems. Implementations of cellular automata and artificial neural networks were described and created with that method. Guidance from philosophy were helpful in these first studies focusing on programming and feasibility. A rigorous mathematical formalism, however, is still missing. This would not only more precisely describe and define the system metamodel, it would also further generalise it and with that extend its reach to formal treatment in applied mathematics and theoretical aspects of computational science as well as extend its applicability to other mathematical and computational models such as agent-based models. Here, a mathematical definition of the system metamodel is provided. Based on the presented formalism, model creation and equivalence of cellular automata and artificial neural networks are proved. It thus provides a formal approach for studying the creation of mathematical models as well as their structural and operational comparison.Comment: 13 pages, 1 tabl

bdbms -- A Database Management System for Biological Data

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US