A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Revising Type-2 Computation and Degrees of Discontinuity

By the sometimes so-called MAIN THEOREM of Recursive Analysis, every computable real function is necessarily continuous. Weihrauch and Zheng (TCS'2000), Brattka (MLQ'2005), and Ziegler (ToCS'2006) have considered different relaxed notions of computability to cover also discontinuous functions. The present work compares and unifies these approaches. This is based on the concept of the JUMP of a representation: both a TTE-counterpart to the well known recursion-theoretic jump on Kleene's Arithmetical Hierarchy of hypercomputation: and a formalization of revising computation in the sense of Shoenfield. We also consider Markov and Banach/Mazur oracle-computation of discontinuous fu nctions and characterize the computational power of Type-2 nondeterminism to coincide with the first level of the Analytical Hierarchy.Comment: to appear in Proc. CCA'0

Further developments in generating type-safe messaging

At ICALEPCS '09, we introduced a source code generator that allows processes to communicate safely using data types native to each host language. In this paper, we discuss further development that has occurred since the conference in Kobe, Japan, including the addition of three more client languages, an optimization in network packet size and the addition of a new protocol data type.Comment: 4 pp. 13th International Conference on Accelerator and Large Experimental Physics Control Systems (ICALEPCS 2011). 10-14 Oct 2011. Grenoble, Franc

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