2,623 research outputs found
Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules
Markov state models (MSMs) have been successful in computing metastable
states, slow relaxation timescales and associated structural changes, and
stationary or kinetic experimental observables of complex molecules from large
amounts of molecular dynamics simulation data. However, MSMs approximate the
true dynamics by assuming a Markov chain on a clusters discretization of the
state space. This approximation is difficult to make for high-dimensional
biomolecular systems, and the quality and reproducibility of MSMs has therefore
been limited. Here, we discard the assumption that dynamics are Markovian on
the discrete clusters. Instead, we only assume that the full phase- space
molecular dynamics is Markovian, and a projection of this full dynamics is
observed on the discrete states, leading to the concept of Projected Markov
Models (PMMs). Robust estimation methods for PMMs are not yet available, but we
derive a practically feasible approximation via Hidden Markov Models (HMMs). It
is shown how various molecular observables of interest that are often computed
from MSMs can be computed from HMMs / PMMs. The new framework is applicable to
both, simulation and single-molecule experimental data. We demonstrate its
versatility by applications to educative model systems, an 1 ms Anton MD
simulation of the BPTI protein, and an optical tweezer force probe trajectory
of an RNA hairpin
A Unifying review of linear gaussian models
Factor analysis, principal component analysis, mixtures of gaussian clusters, vector quantization, Kalman filter models, and hidden Markov models can all be unified as variations of unsupervised learning under a single basic generative model. This is achieved by collecting together disparate observations and derivations made by many previous authors and introducing a new way of linking discrete and continuous state models using a simple nonlinearity. Through the use of other nonlinearities, we show how independent component analysis is also a variation of the same basic generative model.We show that factor analysis and mixtures of gaussians can be implemented in autoencoder neural networks and learned using squared error plus the same regularization term. We introduce a new model for static data, known as sensible principal component analysis, as well as a novel concept of spatially adaptive observation noise. We also review some of the literature involving global and local mixtures of the basic models and provide pseudocode for inference and learning for all the basic models
Lumpable hidden Markov models - model reduction and reduced complexity filtering
Copyright © 2000 IEEEThis paper is concerned with filtering of hidden Markov processes (HMP) which possess (or approximately possess) the property of lumpability. This property is a generalization of the property of lumpability of a Markov chain which has been previously addressed by others. In essence, the property of lumpability means that there is a partition of the (atomic) states of the Markov chain into aggregated sets which act in a similar manner as far as the state dynamics and observation statistics are concerned. We prove necessary and sufficient conditions on the HMP for exact lumpability to hold. For a particular class of hidden Markov models (HMM), namely finite output alphabet models, conditions for lumpability of all HMP representable by a specified HMM are given. The corresponding optimal filter algorithms for the aggregated states are then derived. The paper also describes an approach to efficient suboptimal filtering for HMP which are approximately lumpable. By this we mean that the HMM generating the process may be approximated by a lumpable HMM. This approach involves directly finding a lumped HMM which approximates the original HMM well, in a matrix norm sense. An alternative approach for model reduction based on approximating a given HMM by an exactly lumpable HMM is also derived. This method is based on the alternating convex projections algorithm. Some simulation examples are presented which illustrate the performance of the suboptimal filtering algorithmsLangford B. White, Robert Mahony and Gary D. Brush
Hyperspectral Unmixing Overview: Geometrical, Statistical, and Sparse Regression-Based Approaches
Imaging spectrometers measure electromagnetic energy scattered in their
instantaneous field view in hundreds or thousands of spectral channels with
higher spectral resolution than multispectral cameras. Imaging spectrometers
are therefore often referred to as hyperspectral cameras (HSCs). Higher
spectral resolution enables material identification via spectroscopic analysis,
which facilitates countless applications that require identifying materials in
scenarios unsuitable for classical spectroscopic analysis. Due to low spatial
resolution of HSCs, microscopic material mixing, and multiple scattering,
spectra measured by HSCs are mixtures of spectra of materials in a scene. Thus,
accurate estimation requires unmixing. Pixels are assumed to be mixtures of a
few materials, called endmembers. Unmixing involves estimating all or some of:
the number of endmembers, their spectral signatures, and their abundances at
each pixel. Unmixing is a challenging, ill-posed inverse problem because of
model inaccuracies, observation noise, environmental conditions, endmember
variability, and data set size. Researchers have devised and investigated many
models searching for robust, stable, tractable, and accurate unmixing
algorithms. This paper presents an overview of unmixing methods from the time
of Keshava and Mustard's unmixing tutorial [1] to the present. Mixing models
are first discussed. Signal-subspace, geometrical, statistical, sparsity-based,
and spatial-contextual unmixing algorithms are described. Mathematical problems
and potential solutions are described. Algorithm characteristics are
illustrated experimentally.Comment: This work has been accepted for publication in IEEE Journal of
Selected Topics in Applied Earth Observations and Remote Sensin
Herding as a Learning System with Edge-of-Chaos Dynamics
Herding defines a deterministic dynamical system at the edge of chaos. It
generates a sequence of model states and parameters by alternating parameter
perturbations with state maximizations, where the sequence of states can be
interpreted as "samples" from an associated MRF model. Herding differs from
maximum likelihood estimation in that the sequence of parameters does not
converge to a fixed point and differs from an MCMC posterior sampling approach
in that the sequence of states is generated deterministically. Herding may be
interpreted as a"perturb and map" method where the parameter perturbations are
generated using a deterministic nonlinear dynamical system rather than randomly
from a Gumbel distribution. This chapter studies the distinct statistical
characteristics of the herding algorithm and shows that the fast convergence
rate of the controlled moments may be attributed to edge of chaos dynamics. The
herding algorithm can also be generalized to models with latent variables and
to a discriminative learning setting. The perceptron cycling theorem ensures
that the fast moment matching property is preserved in the more general
framework
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