22,984 research outputs found
Inferring hidden Markov models from noisy time sequences: a method to alleviate degeneracy in molecular dynamics
We present a new method for inferring hidden Markov models from noisy time
sequences without the necessity of assuming a model architecture, thus allowing
for the detection of degenerate states. This is based on the statistical
prediction techniques developed by Crutchfield et al., and generates so called
causal state models, equivalent to hidden Markov models. This method is
applicable to any continuous data which clusters around discrete values and
exhibits multiple transitions between these values such as tethered particle
motion data or Fluorescence Resonance Energy Transfer (FRET) spectra. The
algorithms developed have been shown to perform well on simulated data,
demonstrating the ability to recover the model used to generate the data under
high noise, sparse data conditions and the ability to infer the existence of
degenerate states. They have also been applied to new experimental FRET data of
Holliday Junction dynamics, extracting the expected two state model and
providing values for the transition rates in good agreement with previous
results and with results obtained using existing maximum likelihood based
methods.Comment: 19 pages, 9 figure
The Computational Structure of Spike Trains
Neurons perform computations, and convey the results of those computations
through the statistical structure of their output spike trains. Here we present
a practical method, grounded in the information-theoretic analysis of
prediction, for inferring a minimal representation of that structure and for
characterizing its complexity. Starting from spike trains, our approach finds
their causal state models (CSMs), the minimal hidden Markov models or
stochastic automata capable of generating statistically identical time series.
We then use these CSMs to objectively quantify both the generalizable structure
and the idiosyncratic randomness of the spike train. Specifically, we show that
the expected algorithmic information content (the information needed to
describe the spike train exactly) can be split into three parts describing (1)
the time-invariant structure (complexity) of the minimal spike-generating
process, which describes the spike train statistically; (2) the randomness
(internal entropy rate) of the minimal spike-generating process; and (3) a
residual pure noise term not described by the minimal spike-generating process.
We use CSMs to approximate each of these quantities. The CSMs are inferred
nonparametrically from the data, making only mild regularity assumptions, via
the causal state splitting reconstruction algorithm. The methods presented here
complement more traditional spike train analyses by describing not only spiking
probability and spike train entropy, but also the complexity of a spike train's
structure. We demonstrate our approach using both simulated spike trains and
experimental data recorded in rat barrel cortex during vibrissa stimulation.Comment: Somewhat different format from journal version but same conten
Structure and Randomness of Continuous-Time Discrete-Event Processes
Loosely speaking, the Shannon entropy rate is used to gauge a stochastic
process' intrinsic randomness; the statistical complexity gives the cost of
predicting the process. We calculate, for the first time, the entropy rate and
statistical complexity of stochastic processes generated by finite unifilar
hidden semi-Markov models---memoryful, state-dependent versions of renewal
processes. Calculating these quantities requires introducing novel mathematical
objects ({\epsilon}-machines of hidden semi-Markov processes) and new
information-theoretic methods to stochastic processes.Comment: 10 pages, 2 figures;
http://csc.ucdavis.edu/~cmg/compmech/pubs/ctdep.ht
Causal Effect Inference with Deep Latent-Variable Models
Learning individual-level causal effects from observational data, such as
inferring the most effective medication for a specific patient, is a problem of
growing importance for policy makers. The most important aspect of inferring
causal effects from observational data is the handling of confounders, factors
that affect both an intervention and its outcome. A carefully designed
observational study attempts to measure all important confounders. However,
even if one does not have direct access to all confounders, there may exist
noisy and uncertain measurement of proxies for confounders. We build on recent
advances in latent variable modeling to simultaneously estimate the unknown
latent space summarizing the confounders and the causal effect. Our method is
based on Variational Autoencoders (VAE) which follow the causal structure of
inference with proxies. We show our method is significantly more robust than
existing methods, and matches the state-of-the-art on previous benchmarks
focused on individual treatment effects.Comment: Published as a conference paper at NIPS 201
Reductions of Hidden Information Sources
In all but special circumstances, measurements of time-dependent processes
reflect internal structures and correlations only indirectly. Building
predictive models of such hidden information sources requires discovering, in
some way, the internal states and mechanisms. Unfortunately, there are often
many possible models that are observationally equivalent. Here we show that the
situation is not as arbitrary as one would think. We show that generators of
hidden stochastic processes can be reduced to a minimal form and compare this
reduced representation to that provided by computational mechanics--the
epsilon-machine. On the way to developing deeper, measure-theoretic foundations
for the latter, we introduce a new two-step reduction process. The first step
(internal-event reduction) produces the smallest observationally equivalent
sigma-algebra and the second (internal-state reduction) removes sigma-algebra
components that are redundant for optimal prediction. For several classes of
stochastic dynamical systems these reductions produce representations that are
equivalent to epsilon-machines.Comment: 12 pages, 4 figures; 30 citations; Updates at
http://www.santafe.edu/~cm
The Origins of Computational Mechanics: A Brief Intellectual History and Several Clarifications
The principle goal of computational mechanics is to define pattern and
structure so that the organization of complex systems can be detected and
quantified. Computational mechanics developed from efforts in the 1970s and
early 1980s to identify strange attractors as the mechanism driving weak fluid
turbulence via the method of reconstructing attractor geometry from measurement
time series and in the mid-1980s to estimate equations of motion directly from
complex time series. In providing a mathematical and operational definition of
structure it addressed weaknesses of these early approaches to discovering
patterns in natural systems.
Since then, computational mechanics has led to a range of results from
theoretical physics and nonlinear mathematics to diverse applications---from
closed-form analysis of Markov and non-Markov stochastic processes that are
ergodic or nonergodic and their measures of information and intrinsic
computation to complex materials and deterministic chaos and intelligence in
Maxwellian demons to quantum compression of classical processes and the
evolution of computation and language.
This brief review clarifies several misunderstandings and addresses concerns
recently raised regarding early works in the field (1980s). We show that
misguided evaluations of the contributions of computational mechanics are
groundless and stem from a lack of familiarity with its basic goals and from a
failure to consider its historical context. For all practical purposes, its
modern methods and results largely supersede the early works. This not only
renders recent criticism moot and shows the solid ground on which computational
mechanics stands but, most importantly, shows the significant progress achieved
over three decades and points to the many intriguing and outstanding challenges
in understanding the computational nature of complex dynamic systems.Comment: 11 pages, 123 citations;
http://csc.ucdavis.edu/~cmg/compmech/pubs/cmr.ht
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