1,238 research outputs found
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
Descriptional complexity of cellular automata and decidability questions
We study the descriptional complexity of cellular automata (CA), a parallel model of computation. We show that between one of the simplest cellular models, the realtime-OCA. and "classical" models like deterministic finite automata (DFA) or pushdown automata (PDA), there will be savings concerning the size of description not bounded by any recursive function, a so-called nonrecursive trade-off. Furthermore, nonrecursive trade-offs are shown between some restricted classes of cellular automata. The set of valid computations of a Turing machine can be recognized by a realtime-OCA. This implies that many decidability questions are not even semi decidable for cellular automata. There is no pumping lemma and no minimization algorithm for cellular automata
Transition between immune and disease states in a cellular automaton model of clonal immune response
In this paper we extend the Celada-Seiden (CS) model of the humoral immune
response to include infectious virus and cytotoxic T lymphocytes (cellular
response). The response of the system to virus involves a competition between
the ability of the virus to kill the host cells and the host's ability to
eliminate the virus. We find two basins of attraction in the dynamics of this
system, one is identified with disease and the other with the immune state.
There is also an oscillating state that exists on the border of these two
stable states. Fluctuations in the population of virus or antibody can end the
oscillation and drive the system into one of the stable states. The
introduction of mechanisms of cross-regulation between the two responses can
bias the system towards one of them. We also study a mean field model, based on
coupled maps, to investigate virus-like infections. This simple model
reproduces the attractors for average populations observed in the cellular
automaton. All the dynamical behavior connected to spatial extension is lost,
as is the oscillating feature. Thus the mean field approximation introduced
with coupled maps destroys oscillations.Comment: 27 pages LaTeX + 7 Figures Postscrip
Automatic Filters for the Detection of Coherent Structure in Spatiotemporal Systems
Most current methods for identifying coherent structures in
spatially-extended systems rely on prior information about the form which those
structures take. Here we present two new approaches to automatically filter the
changing configurations of spatial dynamical systems and extract coherent
structures. One, local sensitivity filtering, is a modification of the local
Lyapunov exponent approach suitable to cellular automata and other discrete
spatial systems. The other, local statistical complexity filtering, calculates
the amount of information needed for optimal prediction of the system's
behavior in the vicinity of a given point. By examining the changing
spatiotemporal distributions of these quantities, we can find the coherent
structures in a variety of pattern-forming cellular automata, without needing
to guess or postulate the form of that structure. We apply both filters to
elementary and cyclical cellular automata (ECA and CCA) and find that they
readily identify particles, domains and other more complicated structures. We
compare the results from ECA with earlier ones based upon the theory of formal
languages, and the results from CCA with a more traditional approach based on
an order parameter and free energy. While sensitivity and statistical
complexity are equally adept at uncovering structure, they are based on
different system properties (dynamical and probabilistic, respectively), and
provide complementary information.Comment: 16 pages, 21 figures. Figures considerably compressed to fit arxiv
requirements; write first author for higher-resolution version
Graph Kernels
We present a unified framework to study graph kernels, special cases of which include the random
walk (GƤrtner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004;
MahƩ et al., 2004) graph kernels. Through reduction to a Sylvester equation we improve the time
complexity of kernel computation between unlabeled graphs with n vertices from O(n^6) to O(n^3).
We find a spectral decomposition approach even more efficient when computing entire kernel matrices.
For labeled graphs we develop conjugate gradient and fixed-point methods that take O(dn^3)
time per iteration, where d is the size of the label set. By extending the necessary linear algebra to
Reproducing Kernel Hilbert Spaces (RKHS) we obtain the same result for d-dimensional edge kernels,
and O(n^4) in the infinite-dimensional case; on sparse graphs these algorithms only take O(n^2)
time per iteration in all cases. Experiments on graphs from bioinformatics and other application
domains show that these techniques can speed up computation of the kernel by an order of magnitude
or more. We also show that certain rational kernels (Cortes et al., 2002, 2003, 2004) when
specialized to graphs reduce to our random walk graph kernel. Finally, we relate our framework to
R-convolution kernels (Haussler, 1999) and provide a kernel that is close to the optimal assignment
kernel of Frƶhlich et al. (2006) yet provably positive semi-definite
A single-shot measurement of the energy of product states in a translation invariant spin chain can replace any quantum computation
In measurement-based quantum computation, quantum algorithms are implemented
via sequences of measurements. We describe a translationally invariant
finite-range interaction on a one-dimensional qudit chain and prove that a
single-shot measurement of the energy of an appropriate computational basis
state with respect to this Hamiltonian provides the output of any quantum
circuit. The required measurement accuracy scales inverse polynomially with the
size of the simulated quantum circuit. This shows that the implementation of
energy measurements on generic qudit chains is as hard as the realization of
quantum computation. Here a ''measurement'' is any procedure that samples from
the spectral measure induced by the observable and the state under
consideration. As opposed to measurement-based quantum computation, the
post-measurement state is irrelevant.Comment: 19 pages, transition rules for the CA correcte
An Individual-based Probabilistic Model for Fish Stock Simulation
We define an individual-based probabilistic model of a sole (Solea solea)
behaviour. The individual model is given in terms of an Extended Probabilistic
Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the
paper and that is shown to be interpretable as a Markov decision process. A
given EPDTA model can be probabilistically model-checked by giving a suitable
translation into syntax accepted by existing model-checkers. In order to
simulate the dynamics of a given population of soles in different environmental
scenarios, an agent-based simulation environment is defined in which each agent
implements the behaviour of the given EPDTA model. By varying the probabilities
and the characteristic functions embedded in the EPDTA model it is possible to
represent different scenarios and to tune the model itself by comparing the
results of the simulations with real data about the sole stock in the North
Adriatic sea, available from the recent project SoleMon. The simulator is
presented and made available for its adaptation to other species.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314
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