1,386 research outputs found
Experiment-friendly kinetic analysis of single molecule data in and out of equilibrium
We present a simple and robust technique to extract kinetic rate models and
thermodynamic quantities from single molecule time traces. SMACKS (Single
Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood
approach that works equally well for long trajectories as for a set of short
ones. It resolves all statistically relevant rates and also their
uncertainties. This is achieved by optimizing one global kinetic model based on
the complete dataset, while allowing for experimental variations between
individual trajectories. In particular, neither a priori models nor equilibrium
have to be assumed. The power of SMACKS is demonstrated on the kinetics of the
multi-domain protein Hsp90 measured by smFRET (single molecule F\"orster
resonance energy transfer). Experiments in and out of equilibrium are analyzed
and compared to simulations, shedding new light on the role of Hsp90's ATPase
function. SMACKS pushes the boundaries of single molecule kinetics far beyond
current methods.Comment: 11 pages, 8 figure
S-estimation of hidden Markov models
A method for robust estimation of dynamic mixtures of multivariate distributions is proposed. The EM algorithm is modified by replacing the classical M-step
with high breakdown S-estimation of location and scatter, performed by using the
bisquare multivariate S-estimator. Estimates are obtained by solving a system of estimating equations that are characterized by component specific sets of weights, based on
robust Mahalanobis-type distances. Convergence of the resulting algorithm is proved
and its finite sample behavior is investigated by means of a brief simulation study and
n application to a multivariate time series of daily returns for seven stock markets
Fast, Robust, and Versatile Event Detection through HMM Belief State Gradient Measures
Event detection is a critical feature in data-driven systems as it assists
with the identification of nominal and anomalous behavior. Event detection is
increasingly relevant in robotics as robots operate with greater autonomy in
increasingly unstructured environments. In this work, we present an accurate,
robust, fast, and versatile measure for skill and anomaly identification. A
theoretical proof establishes the link between the derivative of the
log-likelihood of the HMM filtered belief state and the latest emission
probabilities. The key insight is the inverse relationship in which gradient
analysis is used for skill and anomaly identification. Our measure showed
better performance across all metrics than related state-of-the art works. The
result is broadly applicable to domains that use HMMs for event detection.Comment: 8 pages, 7 figures, double col, ieee conference forma
Continuous Action Recognition Based on Sequence Alignment
Continuous action recognition is more challenging than isolated recognition
because classification and segmentation must be simultaneously carried out. We
build on the well known dynamic time warping (DTW) framework and devise a novel
visual alignment technique, namely dynamic frame warping (DFW), which performs
isolated recognition based on per-frame representation of videos, and on
aligning a test sequence with a model sequence. Moreover, we propose two
extensions which enable to perform recognition concomitant with segmentation,
namely one-pass DFW and two-pass DFW. These two methods have their roots in the
domain of continuous recognition of speech and, to the best of our knowledge,
their extension to continuous visual action recognition has been overlooked. We
test and illustrate the proposed techniques with a recently released dataset
(RAVEL) and with two public-domain datasets widely used in action recognition
(Hollywood-1 and Hollywood-2). We also compare the performances of the proposed
isolated and continuous recognition algorithms with several recently published
methods
Greedy Methods in Plume Detection, Localization and Tracking
Greedy method, as an efficient computing tool, can be applied to various combinatorial or nonlinear optimization problems where finding the global optimum is difficult, if not computationally infeasible. A greedy algorithm has the nature of making the locally optimal choice at each stage and then solving the subproblems that arise later. It iteratively make
The path inference filter: model-based low-latency map matching of probe vehicle data
We consider the problem of reconstructing vehicle trajectories from sparse
sequences of GPS points, for which the sampling interval is between 10 seconds
and 2 minutes. We introduce a new class of algorithms, called altogether path
inference filter (PIF), that maps GPS data in real time, for a variety of
trade-offs and scenarios, and with a high throughput. Numerous prior approaches
in map-matching can be shown to be special cases of the path inference filter
presented in this article. We present an efficient procedure for automatically
training the filter on new data, with or without ground truth observations. The
framework is evaluated on a large San Francisco taxi dataset and is shown to
improve upon the current state of the art. This filter also provides insights
about driving patterns of drivers. The path inference filter has been deployed
at an industrial scale inside the Mobile Millennium traffic information system,
and is used to map fleets of data in San Francisco, Sacramento, Stockholm and
Porto.Comment: Preprint, 23 pages and 23 figure
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