476 research outputs found
Weighted ancestors in suffix trees
The classical, ubiquitous, predecessor problem is to construct a data
structure for a set of integers that supports fast predecessor queries. Its
generalization to weighted trees, a.k.a. the weighted ancestor problem, has
been extensively explored and successfully reduced to the predecessor problem.
It is known that any solution for both problems with an input set from a
polynomially bounded universe that preprocesses a weighted tree in O(n
polylog(n)) space requires \Omega(loglogn) query time. Perhaps the most
important and frequent application of the weighted ancestors problem is for
suffix trees. It has been a long-standing open question whether the weighted
ancestors problem has better bounds for suffix trees. We answer this question
positively: we show that a suffix tree built for a text w[1..n] can be
preprocessed using O(n) extra space, so that queries can be answered in O(1)
time. Thus we improve the running times of several applications. Our
improvement is based on a number of data structure tools and a
periodicity-based insight into the combinatorial structure of a suffix tree.Comment: 27 pages, LNCS format. A condensed version will appear in ESA 201
Lower Bounds for Structuring Unreliable Radio Networks
In this paper, we study lower bounds for randomized solutions to the maximal
independent set (MIS) and connected dominating set (CDS) problems in the dual
graph model of radio networks---a generalization of the standard graph-based
model that now includes unreliable links controlled by an adversary. We begin
by proving that a natural geographic constraint on the network topology is
required to solve these problems efficiently (i.e., in time polylogarthmic in
the network size). We then prove the importance of the assumption that nodes
are provided advance knowledge of their reliable neighbors (i.e, neighbors
connected by reliable links). Combined, these results answer an open question
by proving that the efficient MIS and CDS algorithms from [Censor-Hillel, PODC
2011] are optimal with respect to their dual graph model assumptions. They also
provide insight into what properties of an unreliable network enable efficient
local computation.Comment: An extended abstract of this work appears in the 2014 proceedings of
the International Symposium on Distributed Computing (DISC
One-dimensional staged self-assembly
17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011. ProceedingsWe introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest stages is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(logn)-approximable problem). Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of Ω √n/log n even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice
Computing in Additive Networks with Bounded-Information Codes
This paper studies the theory of the additive wireless network model, in
which the received signal is abstracted as an addition of the transmitted
signals. Our central observation is that the crucial challenge for computing in
this model is not high contention, as assumed previously, but rather
guaranteeing a bounded amount of \emph{information} in each neighborhood per
round, a property that we show is achievable using a new random coding
technique.
Technically, we provide efficient algorithms for fundamental distributed
tasks in additive networks, such as solving various symmetry breaking problems,
approximating network parameters, and solving an \emph{asymmetry revealing}
problem such as computing a maximal input.
The key method used is a novel random coding technique that allows a node to
successfully decode the received information, as long as it does not contain
too many distinct values. We then design our algorithms to produce a limited
amount of information in each neighborhood in order to leverage our enriched
toolbox for computing in additive networks
Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
We study the approximate string matching and regular expression matching
problem for the case when the text to be searched is compressed with the
Ziv-Lempel adaptive dictionary compression schemes. We present a time-space
trade-off that leads to algorithms improving the previously known complexities
for both problems. In particular, we significantly improve the space bounds,
which in practical applications are likely to be a bottleneck
Lossless fault-tolerant data structures with additive overhead
12th International Symposium, WADS 2011, New York, NY, USA, August 15-17, 2011. ProceedingsWe develop the first dynamic data structures that tolerate δ memory faults, lose no data, and incur only an O(δ ) additive overhead in overall space and time per operation. We obtain such data structures for arrays, linked lists, binary search trees, interval trees, predecessor search, and suffix trees. Like previous data structures, δ must be known in advance, but we show how to restore pristine state in linear time, in parallel with queries, making δ just a bound on the rate of memory faults. Our data structures require Θ(δ) words of safe memory during an operation, which may not be theoretically necessary but seems a practical assumption.Center for Massive Data Algorithmics (MADALGO
Cross-Document Pattern Matching
We study a new variant of the string matching problem called cross-document
string matching, which is the problem of indexing a collection of documents to
support an efficient search for a pattern in a selected document, where the
pattern itself is a substring of another document. Several variants of this
problem are considered, and efficient linear-space solutions are proposed with
query time bounds that either do not depend at all on the pattern size or
depend on it in a very limited way (doubly logarithmic). As a side result, we
propose an improved solution to the weighted level ancestor problem
Suffix Tree of Alignment: An Efficient Index for Similar Data
We consider an index data structure for similar strings. The generalized
suffix tree can be a solution for this. The generalized suffix tree of two
strings and is a compacted trie representing all suffixes in and
. It has leaves and can be constructed in time.
However, if the two strings are similar, the generalized suffix tree is not
efficient because it does not exploit the similarity which is usually
represented as an alignment of and .
In this paper we propose a space/time-efficient suffix tree of alignment
which wisely exploits the similarity in an alignment. Our suffix tree for an
alignment of and has leaves where is the sum of
the lengths of all parts of different from and is the sum of the
lengths of some common parts of and . We did not compromise the pattern
search to reduce the space. Our suffix tree can be searched for a pattern
in time where is the number of occurrences of in and
. We also present an efficient algorithm to construct the suffix tree of
alignment. When the suffix tree is constructed from scratch, the algorithm
requires time where is the sum of the lengths
of other common substrings of and . When the suffix tree of is
already given, it requires time.Comment: 12 page
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