10,901 research outputs found
Log-domain implementation of complex dynamics reaction-diffusion neural networks
In this paper, we have identified a second-order reaction-diffusion differential equation able to reproduce through parameter setting different complex spatio-temporal behaviors. We have designed a log-domain hardware that implements the spatially discretized version of the selected reaction-diffusion equation. The logarithmic compression of the state variables allows several decades of variation of these state variables within subthreshold operation of the MOS transistors. Furthermore, as all the equation parameters are implemented as currents, they can be adjusted several decades. As a demonstrator, we have designed a chip containing a linear array of ten second-order dynamics coupled cells. Using this hardware, we have experimentally reproduced two complex spatio-temporal phenomena: the propagation of travelling waves and of trigger waves, as well as isolated oscillatory cells.Gobierno de España TIC1999-0446-C02-02Office of Naval Research (USA
Real-Time Anisotropic Diffusion using Space-Variant Vision
Many computer and robot vision applications require multi-scale image analysis. Classically, this has been accomplished through the use of a linear scale-space, which is constructed by convolution of visual input with Gaussian kernels of varying size (scale). This has been shown to be equivalent to the solution of a linear diffusion equation on an infinite domain, as the Gaussian is the Green's function of such a system (Koenderink, 1984). Recently, much work has been focused on the use of a variable conductance function resulting in anisotropic diffusion described by a nonlinear partial differential equation (PDF). The use of anisotropic diffusion with a conductance coefficient which is a decreasing function of the gradient magnitude has been shown to enhance edges, while decreasing some types of noise (Perona and Malik, 1987). Unfortunately, the solution of the anisotropic diffusion equation requires the numerical integration of a nonlinear PDF which is a costly process when carried out on a fixed mesh such as a typical image. In this paper we show that the complex log transformation, variants of which are universally used in mammalian retino-cortical systems, allows the nonlinear diffusion equation to be integrated at exponentially enhanced rates due to the non-uniform mesh spacing inherent in the log domain. The enhanced integration rates, coupled with the intrinsic compression of the complex log transformation, yields a seed increase of between two and three orders of magnitude, providing a means of performing real-time image enhancement using anisotropic diffusion.Office of Naval Research (N00014-95-I-0409
Evidence accumulation in a Laplace domain decision space
Evidence accumulation models of simple decision-making have long assumed that
the brain estimates a scalar decision variable corresponding to the
log-likelihood ratio of the two alternatives. Typical neural implementations of
this algorithmic cognitive model assume that large numbers of neurons are each
noisy exemplars of the scalar decision variable. Here we propose a neural
implementation of the diffusion model in which many neurons construct and
maintain the Laplace transform of the distance to each of the decision bounds.
As in classic findings from brain regions including LIP, the firing rate of
neurons coding for the Laplace transform of net accumulated evidence grows to a
bound during random dot motion tasks. However, rather than noisy exemplars of a
single mean value, this approach makes the novel prediction that firing rates
grow to the bound exponentially, across neurons there should be a distribution
of different rates. A second set of neurons records an approximate inversion of
the Laplace transform, these neurons directly estimate net accumulated
evidence. In analogy to time cells and place cells observed in the hippocampus
and other brain regions, the neurons in this second set have receptive fields
along a "decision axis." This finding is consistent with recent findings from
rodent recordings. This theoretical approach places simple evidence
accumulation models in the same mathematical language as recent proposals for
representing time and space in cognitive models for memory.Comment: Revised for CB
Coarse-grained dynamics of an activity bump in a neural field model
We study a stochastic nonlocal PDE, arising in the context of modelling
spatially distributed neural activity, which is capable of sustaining
stationary and moving spatially-localized ``activity bumps''. This system is
known to undergo a pitchfork bifurcation in bump speed as a parameter (the
strength of adaptation) is changed; yet increasing the noise intensity
effectively slowed the motion of the bump. Here we revisit the system from the
point of view of describing the high-dimensional stochastic dynamics in terms
of the effective dynamics of a single scalar "coarse" variable. We show that
such a reduced description in the form of an effective Langevin equation
characterized by a double-well potential is quantitatively successful. The
effective potential can be extracted using short, appropriately-initialized
bursts of direct simulation. We demonstrate this approach in terms of (a) an
experience-based "intelligent" choice of the coarse observable and (b) an
observable obtained through data-mining direct simulation results, using a
diffusion map approach.Comment: Corrected aknowledgement
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations
Molecular dynamics (MD) simulations can model the interactions between
macromolecules with high spatiotemporal resolution but at a high computational
cost. By combining high-throughput MD with Markov state models (MSMs), it is
now possible to obtain long-timescale behavior of small to intermediate
biomolecules and complexes. To model the interactions of many molecules at
large lengthscales, particle-based reaction-diffusion (RD) simulations are more
suitable but lack molecular detail. Thus, coupling MSMs and RD simulations
(MSM/RD) would be highly desirable, as they could efficiently produce
simulations at large time- and lengthscales, while still conserving the
characteristic features of the interactions observed at atomic detail. While
such a coupling seems straightforward, fundamental questions are still open:
Which definition of MSM states is suitable? Which protocol to merge and split
RD particles in an association/dissociation reaction will conserve the correct
bimolecular kinetics and thermodynamics? In this paper, we make the first step
towards MSM/RD by laying out a general theory of coupling and proposing a first
implementation for association/dissociation of a protein with a small ligand (A
+ B C). Applications on a toy model and CO diffusion into the heme cavity
of myoglobin are reported
The Kinetic Basis of Morphogenesis
It has been shown recently (Shalygo, 2014) that stationary and dynamic
patterns can arise in the proposed one-component model of the analog
(continuous state) kinetic automaton, or kinon for short, defined as a
reflexive dynamical system with active transport. This paper presents
extensions of the model, which increase further its complexity and tunability,
and shows that the extended kinon model can produce spatio-temporal patterns
pertaining not only to pattern formation but also to morphogenesis in real
physical and biological systems. The possible applicability of the model to
morphogenetic engineering and swarm robotics is also discussed.Comment: 8 pages. Submitted to the 13th European Conference on Artificial Life
(ECAL-2015) on March 10, 2015. Accepted on April 28, 201
Augmenting Physical Models with Deep Networks for Complex Dynamics Forecasting
Forecasting complex dynamical phenomena in settings where only partial
knowledge of their dynamics is available is a prevalent problem across various
scientific fields. While purely data-driven approaches are arguably
insufficient in this context, standard physical modeling based approaches tend
to be over-simplistic, inducing non-negligible errors. In this work, we
introduce the APHYNITY framework, a principled approach for augmenting
incomplete physical dynamics described by differential equations with deep
data-driven models. It consists in decomposing the dynamics into two
components: a physical component accounting for the dynamics for which we have
some prior knowledge, and a data-driven component accounting for errors of the
physical model. The learning problem is carefully formulated such that the
physical model explains as much of the data as possible, while the data-driven
component only describes information that cannot be captured by the physical
model, no more, no less. This not only provides the existence and uniqueness
for this decomposition, but also ensures interpretability and benefits
generalization. Experiments made on three important use cases, each
representative of a different family of phenomena, i.e. reaction-diffusion
equations, wave equations and the non-linear damped pendulum, show that
APHYNITY can efficiently leverage approximate physical models to accurately
forecast the evolution of the system and correctly identify relevant physical
parameters
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