Sorry, you need to enable JavaScript to visit this website.

Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this case, which Rossi et al. recently implemented, but it uses two passes over the patterns and buffers a pointer for each character during the first pass. In this paper, we simplify their solution and make it streaming, at the cost of slowing it down slightly.

Categories:
57 Views

We present a representation of trajectories moving through the space without any constraint. It combines an in-memory cached index based on compact data structures and a classic disk-based strategy. The first structure allows some loss of precision that is refined with the second component. This approach reduces the number of accesses to disk. Comparing it with a classical index like the MVR-tree, this structure obtains competitive times in queries like time slice and knn, and sharply outperforms it in time interval queries.

Categories:
13 Views

Fast data streams are applied by various applications such as multimedia, communication and sensory devices. The amount of data is getting larger and the transfer speed is also getting higher. To address this kind of fast applications, a high performance stream-based data compression mechanism is demanded.

Categories:
73 Views

We consider the problem of compact representation of graphs with small bandwidth as well as graphs with small treedepth. These parameters capture structural properties of graphs that come in useful in certain applications.

Categories:
66 Views

Recent hardware advances in quantum and quantum-inspired annealers promise substantial speedup for solving NP-hard combinatorial optimization problems compared to general-purpose computers. These special-purpose hardware are built for solving hard instances of Quadratic Unconstrained Binary Optimization (QUBO) problems. In terms of number of variables and precision of these hardware are usually resource-constrained and they work either in Ising space $\ising$ or in Boolean space $\bool$. Many naturally occurring problem instances are higher-order in nature.

Categories:
34 Views

Given a dynamic set K of k strings of total length n whose characters are drawn from an alphabet of size σ, a keyword dictionary is a data structure built on K that provides locate, prefix search, and update operations on K. Under the assumption that α = w / lg σ characters fit into a single machine word w, we propose a keyword dictionary that represents K in n lg σ + O(k lg n) bits of space, supporting all operations in O(m / α + lg α) expected time on an input string of length m in the word RAM model.

Categories:
104 Views

Re-Pair is a grammar compression scheme with favorably good compression rates. The computation of Re-Pair comes with the cost of maintaining large frequency tables, which makes it hard to compute Re-Pair on large scale data sets. As a solution for this problem we present, given a text of length n whose characters are drawn from an integer alphabet, an O(n^2) time algorithm computing Re-Pair in n lg max(n, τ) bits of working space including the text space, where τ is the number of terminals and non-terminals.

Categories:
72 Views

Pages