3,248 research outputs found
String Synchronizing Sets: Sublinear-Time BWT Construction and Optimal LCE Data Structure
Burrows-Wheeler transform (BWT) is an invertible text transformation that,
given a text of length , permutes its symbols according to the
lexicographic order of suffixes of . BWT is one of the most heavily studied
algorithms in data compression with numerous applications in indexing, sequence
analysis, and bioinformatics. Its construction is a bottleneck in many
scenarios, and settling the complexity of this task is one of the most
important unsolved problems in sequence analysis that has remained open for 25
years. Given a binary string of length , occupying machine
words, the BWT construction algorithm due to Hon et al. (SIAM J. Comput., 2009)
runs in time and space. Recent advancements (Belazzougui,
STOC 2014, and Munro et al., SODA 2017) focus on removing the alphabet-size
dependency in the time complexity, but they still require time.
In this paper, we propose the first algorithm that breaks the -time
barrier for BWT construction. Given a binary string of length , our
procedure builds the Burrows-Wheeler transform in time and
space. We complement this result with a conditional lower bound
proving that any further progress in the time complexity of BWT construction
would yield faster algorithms for the very well studied problem of counting
inversions: it would improve the state-of-the-art -time
solution by Chan and P\v{a}tra\c{s}cu (SODA 2010). Our algorithm is based on a
novel concept of string synchronizing sets, which is of independent interest.
As one of the applications, we show that this technique lets us design a data
structure of the optimal size that answers Longest Common
Extension queries (LCE queries) in time and, furthermore, can be
deterministically constructed in the optimal time.Comment: Full version of a paper accepted to STOC 201
Toward a Formal Semantics for Autonomic Components
Autonomic management can improve the QoS provided by parallel/ distributed
applications. Within the CoreGRID Component Model, the autonomic management is
tailored to the automatic - monitoring-driven - alteration of the component
assembly and, therefore, is defined as the effect of (distributed) management
code. This work yields a semantics based on hypergraph rewriting suitable to
model the dynamic evolution and non-functional aspects of Service Oriented
Architectures and component-based autonomic applications. In this regard, our
main goal is to provide a formal description of adaptation operations that are
typically only informally specified. We contend that our approach makes easier
to raise the level of abstraction of management code in autonomic and adaptive
applications.Comment: 11 pages + cover pag
Efficient String Matching on Coded Texts
The so called "four Russians technique'' is often used to speed up algorithms by encoding several data items in a single memory cell. Given a sequence of n symbols over a constant size alphabet, one can encode the sequence into O(n / lambda) memory cells in O(log(lambda) ) time using n / log(lambda) processors. This paper presents an efficient CRCW-PRAM string-matching algorithm for coded texts that takes O(log log(m/lambda)) time making only O(n / lambda ) operations, an improvement by a factor of lambda = O(log n) on the number of operations used in previous algorithms. Using this string-matching algorithm one can test if a string is square-free and find all palindromes in a string in O(log log n) time using n / log log n processors
Scalable string reconciliation by recursive content-dependent shingling
We consider the problem of reconciling similar strings in a distributed system. Specifically, we are interested in performing this reconciliation in an efficient manner, minimizing the communication cost. Our problem applies to several types of large-scale distributed networks, file synchronization utilities, and any system that manages the consistency of string encoded ordered data. We present the novel Recursive Content-Dependent Shingling (RCDS) protocol that can handle large strings and has the communication complexity that scales with the edit distance between the reconciling strings. Also, we provide analysis, experimental results, and comparisons to existing synchronization software such as the Rsync utility with an implementation of our protocol.2019-12-03T00:00:00
An Object-Oriented Model for Extensible Concurrent Systems: the Composition-Filters Approach
Applying the object-oriented paradigm for the development of large and complex software systems offers several advantages, of which increased extensibility and reusability are the most prominent ones. The object-oriented model is also quite suitable for modeling concurrent systems. However, it appears that extensibility and reusability of concurrent applications is far from trivial. The problems that arise, the so-called inheritance anomalies are analyzed and presented in this paper. A set of requirements for extensible concurrent languages is formulated. As a solution to the identified problems, an extension to the object-oriented model is presented; composition filters. Composition filters capture messages and can express certain constraints and operations on these messages, for example buffering. In this paper we explain the composition filters approach, demonstrate its expressive power through a number of examples and show that composition filters do not suffer from the inheritance anomalies and fulfill the requirements that were established
26. Theorietag Automaten und Formale Sprachen 23. Jahrestagung Logik in der Informatik: Tagungsband
Der Theorietag ist die Jahrestagung der Fachgruppe Automaten und Formale Sprachen der Gesellschaft für Informatik und fand erstmals 1991 in Magdeburg statt. Seit dem Jahr 1996 wird der Theorietag von einem eintägigen Workshop mit eingeladenen Vorträgen begleitet. Die Jahrestagung der Fachgruppe Logik in der Informatik der Gesellschaft für Informatik fand erstmals 1993 in Leipzig statt. Im Laufe beider Jahrestagungen finden auch die jährliche Fachgruppensitzungen statt. In diesem Jahr wird der Theorietag der Fachgruppe Automaten und Formale Sprachen erstmalig zusammen mit der Jahrestagung der Fachgruppe Logik in der Informatik abgehalten. Organisiert wurde die gemeinsame Veranstaltung von der Arbeitsgruppe Zuverlässige Systeme des Instituts für Informatik an der Christian-Albrechts-Universität Kiel vom 4. bis 7. Oktober im Tagungshotel Tannenfelde bei Neumünster. Während des Tre↵ens wird ein Workshop für alle Interessierten statt finden. In Tannenfelde werden • Christoph Löding (Aachen) • Tomás Masopust (Dresden) • Henning Schnoor (Kiel) • Nicole Schweikardt (Berlin) • Georg Zetzsche (Paris) eingeladene Vorträge zu ihrer aktuellen Arbeit halten. Darüber hinaus werden 26 Vorträge von Teilnehmern und Teilnehmerinnen gehalten, 17 auf dem Theorietag Automaten und formale Sprachen und neun auf der Jahrestagung Logik in der Informatik. Der vorliegende Band enthält Kurzfassungen aller Beiträge. Wir danken der Gesellschaft für Informatik, der Christian-Albrechts-Universität zu Kiel und dem Tagungshotel Tannenfelde für die Unterstützung dieses Theorietags. Ein besonderer Dank geht an das Organisationsteam: Maike Bradler, Philipp Sieweck, Joel Day. Kiel, Oktober 2016 Florin Manea, Dirk Nowotka und Thomas Wilk
Cellular automaton supercolliders
Gliders in one-dimensional cellular automata are compact groups of
non-quiescent and non-ether patterns (ether represents a periodic background)
translating along automaton lattice. They are cellular-automaton analogous of
localizations or quasi-local collective excitations travelling in a spatially
extended non-linear medium. They can be considered as binary strings or symbols
travelling along a one-dimensional ring, interacting with each other and
changing their states, or symbolic values, as a result of interactions. We
analyse what types of interaction occur between gliders travelling on a
cellular automaton `cyclotron' and build a catalog of the most common
reactions. We demonstrate that collisions between gliders emulate the basic
types of interaction that occur between localizations in non-linear media:
fusion, elastic collision, and soliton-like collision. Computational outcomes
of a swarm of gliders circling on a one-dimensional torus are analysed via
implementation of cyclic tag systems
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