263,337 research outputs found
A SIMPLE, GENERAL STRUCTURE FOR TEMPORAL DOMAINS
Much recent research has focused on .the need for, and definitions of, historical (or temporal)
database and information systems to serve expanding information needs in a variety of
applications. Almost all of this research has assumed that the domain of time itself was well-understood,
and some representation for it simply needed to be included in the model to
provide the needed temporal dimension. In this paper we present a simple, set-theoretic
structure for a time domain which is independent of any particular calendric system. We
concentrate on the general structure and operations necessary to support the needs arising in
modelling time in information systems.Information Systems Working Papers Serie
Local Causal States and Discrete Coherent Structures
Coherent structures form spontaneously in nonlinear spatiotemporal systems
and are found at all spatial scales in natural phenomena from laboratory
hydrodynamic flows and chemical reactions to ocean, atmosphere, and planetary
climate dynamics. Phenomenologically, they appear as key components that
organize the macroscopic behaviors in such systems. Despite a century of
effort, they have eluded rigorous analysis and empirical prediction, with
progress being made only recently. As a step in this, we present a formal
theory of coherent structures in fully-discrete dynamical field theories. It
builds on the notion of structure introduced by computational mechanics,
generalizing it to a local spatiotemporal setting. The analysis' main tool
employs the \localstates, which are used to uncover a system's hidden
spatiotemporal symmetries and which identify coherent structures as
spatially-localized deviations from those symmetries. The approach is
behavior-driven in the sense that it does not rely on directly analyzing
spatiotemporal equations of motion, rather it considers only the spatiotemporal
fields a system generates. As such, it offers an unsupervised approach to
discover and describe coherent structures. We illustrate the approach by
analyzing coherent structures generated by elementary cellular automata,
comparing the results with an earlier, dynamic-invariant-set approach that
decomposes fields into domains, particles, and particle interactions.Comment: 27 pages, 10 figures;
http://csc.ucdavis.edu/~cmg/compmech/pubs/dcs.ht
Taming Numbers and Durations in the Model Checking Integrated Planning System
The Model Checking Integrated Planning System (MIPS) is a temporal least
commitment heuristic search planner based on a flexible object-oriented
workbench architecture. Its design clearly separates explicit and symbolic
directed exploration algorithms from the set of on-line and off-line computed
estimates and associated data structures. MIPS has shown distinguished
performance in the last two international planning competitions. In the last
event the description language was extended from pure propositional planning to
include numerical state variables, action durations, and plan quality objective
functions. Plans were no longer sequences of actions but time-stamped
schedules. As a participant of the fully automated track of the competition,
MIPS has proven to be a general system; in each track and every benchmark
domain it efficiently computed plans of remarkable quality. This article
introduces and analyzes the most important algorithmic novelties that were
necessary to tackle the new layers of expressiveness in the benchmark problems
and to achieve a high level of performance. The extensions include critical
path analysis of sequentially generated plans to generate corresponding optimal
parallel plans. The linear time algorithm to compute the parallel plan bypasses
known NP hardness results for partial ordering by scheduling plans with respect
to the set of actions and the imposed precedence relations. The efficiency of
this algorithm also allows us to improve the exploration guidance: for each
encountered planning state the corresponding approximate sequential plan is
scheduled. One major strength of MIPS is its static analysis phase that grounds
and simplifies parameterized predicates, functions and operators, that infers
knowledge to minimize the state description length, and that detects domain
object symmetries. The latter aspect is analyzed in detail. MIPS has been
developed to serve as a complete and optimal state space planner, with
admissible estimates, exploration engines and branching cuts. In the
competition version, however, certain performance compromises had to be made,
including floating point arithmetic, weighted heuristic search exploration
according to an inadmissible estimate and parameterized optimization
Reformulation in planning
Reformulation of a problem is intended to make the problem more amenable to efficient solution. This is equally true in the special case of reformulating a planning problem. This paper considers various ways in which reformulation can be exploited in planning
PDDL2.1: An extension of PDDL for expressing temporal planning domains
In recent years research in the planning community has moved increasingly towards application of planners to realistic problems involving both time and many types of resources. For example, interest in planning demonstrated by the space research community has inspired work in observation scheduling, planetary rover ex ploration and spacecraft control domains. Other temporal and resource-intensive domains including logistics planning, plant control and manufacturing have also helped to focus the community on the modelling and reasoning issues that must be confronted to make planning technology meet the challenges of application. The International Planning Competitions have acted as an important motivating force behind the progress that has been made in planning since 1998. The third competition (held in 2002) set the planning community the challenge of handling time and numeric resources. This necessitated the development of a modelling language capable of expressing temporal and numeric properties of planning domains. In this paper we describe the language, PDDL2.1, that was used in the competition. We describe the syntax of the language, its formal semantics and the validation of concurrent plans. We observe that PDDL2.1 has considerable modelling power --- exceeding the capabilities of current planning technology --- and presents a number of important challenges to the research community
A General Framework for Representing, Reasoning and Querying with Annotated Semantic Web Data
We describe a generic framework for representing and reasoning with annotated
Semantic Web data, a task becoming more important with the recent increased
amount of inconsistent and non-reliable meta-data on the web. We formalise the
annotated language, the corresponding deductive system and address the query
answering problem. Previous contributions on specific RDF annotation domains
are encompassed by our unified reasoning formalism as we show by instantiating
it on (i) temporal, (ii) fuzzy, and (iii) provenance annotations. Moreover, we
provide a generic method for combining multiple annotation domains allowing to
represent, e.g. temporally-annotated fuzzy RDF. Furthermore, we address the
development of a query language -- AnQL -- that is inspired by SPARQL,
including several features of SPARQL 1.1 (subqueries, aggregates, assignment,
solution modifiers) along with the formal definitions of their semantics
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types
Chromatin is a highly compact and dynamic nuclear structure that consists of
DNA and associated proteins. The main organizational unit is the nucleosome,
which consists of a histone octamer with DNA wrapped around it. Histone
proteins are implicated in the regulation of eukaryote genes and they carry
numerous reversible post-translational modifications that control DNA-protein
interactions and the recruitment of chromatin binding proteins.
Heterochromatin, the transcriptionally inactive part of the genome, is densely
packed and contains histone H3 that is methylated at Lys 9 (H3K9me). The
propagation of H3K9me in nucleosomes along the DNA in chromatin is antagonizing
by methylation of H3 Lysine 4 (H3K4me) and acetylations of several lysines,
which is related to euchromatin and active genes. We show that the related
histone modifications form antagonized domains on a coarse scale. These histone
marks are assumed to be initiated within distinct nucleation sites in the DNA
and to propagate bi-directionally. We propose a simple computer model that
simulates the distribution of heterochromatin in human chromosomes. The
simulations are in agreement with previously reported experimental observations
from two different human cell lines. We reproduced different types of barriers
between heterochromatin and euchromatin providing a unified model for their
function. The effect of changes in the nucleation site distribution and of
propagation rates were studied. The former occurs mainly with the aim of
(de-)activation of single genes or gene groups and the latter has the power of
controlling the transcriptional programs of entire chromosomes. Generally, the
regulatory program of gene transcription is controlled by the distribution of
nucleation sites along the DNA string.Comment: 24 pages,9 figures, 1 table + supplementary materia
Upper Bound on the Products of Particle Interactions in Cellular Automata
Particle-like objects are observed to propagate and interact in many
spatially extended dynamical systems. For one of the simplest classes of such
systems, one-dimensional cellular automata, we establish a rigorous upper bound
on the number of distinct products that these interactions can generate. The
upper bound is controlled by the structural complexity of the interacting
particles---a quantity which is defined here and which measures the amount of
spatio-temporal information that a particle stores. Along the way we establish
a number of properties of domains and particles that follow from the
computational mechanics analysis of cellular automata; thereby elucidating why
that approach is of general utility. The upper bound is tested against several
relatively complex domain-particle cellular automata and found to be tight.Comment: 17 pages, 12 figures, 3 tables,
http://www.santafe.edu/projects/CompMech/papers/ub.html V2: References and
accompanying text modified, to comply with legal demands arising from
on-going intellectual property litigation among third parties. V3: Accepted
for publication in Physica D. References added and other small changes made
per referee suggestion
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