4,583 research outputs found
Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments
Optical microscopy provides rich spatio-temporal information characterizing
in vivo molecular motion. However, effective forces and other parameters used
to summarize molecular motion change over time in live cells due to latent
state changes, e.g., changes induced by dynamic micro-environments,
photobleaching, and other heterogeneity inherent in biological processes. This
study focuses on techniques for analyzing Single Particle Tracking (SPT) data
experiencing abrupt state changes. We demonstrate the approach on GFP tagged
chromatids experiencing metaphase in yeast cells and probe the effective forces
resulting from dynamic interactions that reflect the sum of a number of
physical phenomena. State changes are induced by factors such as microtubule
dynamics exerting force through the centromere, thermal polymer fluctuations,
etc. Simulations are used to demonstrate the relevance of the approach in more
general SPT data analyses. Refined force estimates are obtained by adopting and
modifying a nonparametric Bayesian modeling technique, the Hierarchical
Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT
applications. The HDP-SLDS method shows promise in systematically identifying
dynamical regime changes induced by unobserved state changes when the number of
underlying states is unknown in advance (a common problem in SPT applications).
We expand on the relevance of the HDP-SLDS approach, review the relevant
background of Hierarchical Dirichlet Processes, show how to map discrete time
HDP-SLDS models to classic SPT models, and discuss limitations of the approach.
In addition, we demonstrate new computational techniques for tuning
hyperparameters and for checking the statistical consistency of model
assumptions directly against individual experimental trajectories; the
techniques circumvent the need for "ground-truth" and subjective information.Comment: 25 pages, 6 figures. Differs only typographically from PLoS One
publication available freely as an open-access article at
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.013763
Bayesian Nonparametric Unmixing of Hyperspectral Images
Hyperspectral imaging is an important tool in remote sensing, allowing for
accurate analysis of vast areas. Due to a low spatial resolution, a pixel of a
hyperspectral image rarely represents a single material, but rather a mixture
of different spectra. HSU aims at estimating the pure spectra present in the
scene of interest, referred to as endmembers, and their fractions in each
pixel, referred to as abundances. Today, many HSU algorithms have been
proposed, based either on a geometrical or statistical model. While most
methods assume that the number of endmembers present in the scene is known,
there is only little work about estimating this number from the observed data.
In this work, we propose a Bayesian nonparametric framework that jointly
estimates the number of endmembers, the endmembers itself, and their
abundances, by making use of the Indian Buffet Process as a prior for the
endmembers. Simulation results and experiments on real data demonstrate the
effectiveness of the proposed algorithm, yielding results comparable with
state-of-the-art methods while being able to reliably infer the number of
endmembers. In scenarios with strong noise, where other algorithms provide only
poor results, the proposed approach tends to overestimate the number of
endmembers slightly. The additional endmembers, however, often simply represent
noisy replicas of present endmembers and could easily be merged in a
post-processing step
Unsupervised Sparse Dirichlet-Net for Hyperspectral Image Super-Resolution
In many computer vision applications, obtaining images of high resolution in
both the spatial and spectral domains are equally important. However, due to
hardware limitations, one can only expect to acquire images of high resolution
in either the spatial or spectral domains. This paper focuses on hyperspectral
image super-resolution (HSI-SR), where a hyperspectral image (HSI) with low
spatial resolution (LR) but high spectral resolution is fused with a
multispectral image (MSI) with high spatial resolution (HR) but low spectral
resolution to obtain HR HSI. Existing deep learning-based solutions are all
supervised that would need a large training set and the availability of HR HSI,
which is unrealistic. Here, we make the first attempt to solving the HSI-SR
problem using an unsupervised encoder-decoder architecture that carries the
following uniquenesses. First, it is composed of two encoder-decoder networks,
coupled through a shared decoder, in order to preserve the rich spectral
information from the HSI network. Second, the network encourages the
representations from both modalities to follow a sparse Dirichlet distribution
which naturally incorporates the two physical constraints of HSI and MSI.
Third, the angular difference between representations are minimized in order to
reduce the spectral distortion. We refer to the proposed architecture as
unsupervised Sparse Dirichlet-Net, or uSDN. Extensive experimental results
demonstrate the superior performance of uSDN as compared to the
state-of-the-art.Comment: Accepted by The IEEE Conference on Computer Vision and Pattern
Recognition (CVPR 2018, Spotlight
Solving Inverse Problems with Piecewise Linear Estimators: From Gaussian Mixture Models to Structured Sparsity
A general framework for solving image inverse problems is introduced in this
paper. The approach is based on Gaussian mixture models, estimated via a
computationally efficient MAP-EM algorithm. A dual mathematical interpretation
of the proposed framework with structured sparse estimation is described, which
shows that the resulting piecewise linear estimate stabilizes the estimation
when compared to traditional sparse inverse problem techniques. This
interpretation also suggests an effective dictionary motivated initialization
for the MAP-EM algorithm. We demonstrate that in a number of image inverse
problems, including inpainting, zooming, and deblurring, the same algorithm
produces either equal, often significantly better, or very small margin worse
results than the best published ones, at a lower computational cost.Comment: 30 page
Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis
Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light’s diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we’ve termed the interpretation problem
Recovering Latent Signals from a Mixture of Measurements using a Gaussian Process Prior
In sensing applications, sensors cannot always measure the latent quantity of
interest at the required resolution, sometimes they can only acquire a blurred
version of it due the sensor's transfer function. To recover latent signals
when only noisy mixed measurements of the signal are available, we propose the
Gaussian process mixture of measurements (GPMM), which models the latent signal
as a Gaussian process (GP) and allows us to perform Bayesian inference on such
signal conditional to a set of noisy mixture of measurements. We describe how
to train GPMM, that is, to find the hyperparameters of the GP and the mixing
weights, and how to perform inference on the latent signal under GPMM;
additionally, we identify the solution to the underdetermined linear system
resulting from a sensing application as a particular case of GPMM. The proposed
model is validated in the recovery of three signals: a smooth synthetic signal,
a real-world heart-rate time series and a step function, where GPMM
outperformed the standard GP in terms of estimation error, uncertainty
representation and recovery of the spectral content of the latent signal.Comment: Published on IEEE Signal Processing Letters on Dec. 201
The supervised hierarchical Dirichlet process
We propose the supervised hierarchical Dirichlet process (sHDP), a
nonparametric generative model for the joint distribution of a group of
observations and a response variable directly associated with that whole group.
We compare the sHDP with another leading method for regression on grouped data,
the supervised latent Dirichlet allocation (sLDA) model. We evaluate our method
on two real-world classification problems and two real-world regression
problems. Bayesian nonparametric regression models based on the Dirichlet
process, such as the Dirichlet process-generalised linear models (DP-GLM) have
previously been explored; these models allow flexibility in modelling nonlinear
relationships. However, until now, Hierarchical Dirichlet Process (HDP)
mixtures have not seen significant use in supervised problems with grouped data
since a straightforward application of the HDP on the grouped data results in
learnt clusters that are not predictive of the responses. The sHDP solves this
problem by allowing for clusters to be learnt jointly from the group structure
and from the label assigned to each group.Comment: 14 page
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