15,618 research outputs found
Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations
In classification, prior knowledge is incorporated in a Bayesian framework by assuming that the feature-label distribution belongs to an uncertainty class of feature-label distributions governed by a prior distribution. A posterior
distribution is then derived from the prior and the sample data. An optimal Bayesian classifier (OBC) minimizes the expected misclassification error relative to the posterior distribution. From an application perspective, prior
construction is critical
Inferential stability in systems biology
The modern biological sciences are fraught with statistical difficulties. Biomolecular
stochasticity, experimental noise, and the “large p, small n” problem all contribute to
the challenge of data analysis. Nevertheless, we routinely seek to draw robust, meaningful
conclusions from observations. In this thesis, we explore methods for assessing
the effects of data variability upon downstream inference, in an attempt to quantify and
promote the stability of the inferences we make.
We start with a review of existing methods for addressing this problem, focusing upon the
bootstrap and similar methods. The key requirement for all such approaches is a statistical
model that approximates the data generating process.
We move on to consider biomarker discovery problems. We present a novel algorithm for
proposing putative biomarkers on the strength of both their predictive ability and the stability
with which they are selected. In a simulation study, we find our approach to perform
favourably in comparison to strategies that select on the basis of predictive performance
alone.
We then consider the real problem of identifying protein peak biomarkers for HAM/TSP,
an inflammatory condition of the central nervous system caused by HTLV-1 infection.
We apply our algorithm to a set of SELDI mass spectral data, and identify a number of
putative biomarkers. Additional experimental work, together with known results from the
literature, provides corroborating evidence for the validity of these putative biomarkers.
Having focused on static observations, we then make the natural progression to time
course data sets. We propose a (Bayesian) bootstrap approach for such data, and then
apply our method in the context of gene network inference and the estimation of parameters
in ordinary differential equation models. We find that the inferred gene networks
are relatively unstable, and demonstrate the importance of finding distributions of ODE
parameter estimates, rather than single point estimates
Efficient state-space inference of periodic latent force models
Latent force models (LFM) are principled approaches to incorporating solutions to differen-tial equations within non-parametric inference methods. Unfortunately, the developmentand application of LFMs can be inhibited by their computational cost, especially whenclosed-form solutions for the LFM are unavailable, as is the case in many real world prob-lems where these latent forces exhibit periodic behaviour. Given this, we develop a newsparse representation of LFMs which considerably improves their computational efficiency,as well as broadening their applicability, in a principled way, to domains with periodic ornear periodic latent forces. Our approach uses a linear basis model to approximate onegenerative model for each periodic force. We assume that the latent forces are generatedfrom Gaussian process priors and develop a linear basis model which fully expresses thesepriors. We apply our approach to model the thermal dynamics of domestic buildings andshow that it is effective at predicting day-ahead temperatures within the homes. We alsoapply our approach within queueing theory in which quasi-periodic arrival rates are mod-elled as latent forces. In both cases, we demonstrate that our approach can be implemented efficiently using state-space methods which encode the linear dynamic systems via LFMs.Further, we show that state estimates obtained using periodic latent force models can re-duce the root mean squared error to 17% of that from non-periodic models and 27% of thenearest rival approach which is the resonator model (S ̈arkk ̈a et al., 2012; Hartikainen et al.,2012.
Sensitivity analysis of oscillator models in the space of phase-response curves: Oscillators as open systems
Oscillator models are central to the study of system properties such as
entrainment or synchronization. Due to their nonlinear nature, few
system-theoretic tools exist to analyze those models. The paper develops a
sensitivity analysis for phase-response curves, a fundamental one-dimensional
phase reduction of oscillator models. The proposed theoretical and numerical
analysis tools are illustrated on several system-theoretic questions and models
arising in the biology of cellular rhythms
Efficient State-Space Inference of Periodic Latent Force Models
Latent force models (LFM) are principled approaches to incorporating
solutions to differential equations within non-parametric inference methods.
Unfortunately, the development and application of LFMs can be inhibited by
their computational cost, especially when closed-form solutions for the LFM are
unavailable, as is the case in many real world problems where these latent
forces exhibit periodic behaviour. Given this, we develop a new sparse
representation of LFMs which considerably improves their computational
efficiency, as well as broadening their applicability, in a principled way, to
domains with periodic or near periodic latent forces. Our approach uses a
linear basis model to approximate one generative model for each periodic force.
We assume that the latent forces are generated from Gaussian process priors and
develop a linear basis model which fully expresses these priors. We apply our
approach to model the thermal dynamics of domestic buildings and show that it
is effective at predicting day-ahead temperatures within the homes. We also
apply our approach within queueing theory in which quasi-periodic arrival rates
are modelled as latent forces. In both cases, we demonstrate that our approach
can be implemented efficiently using state-space methods which encode the
linear dynamic systems via LFMs. Further, we show that state estimates obtained
using periodic latent force models can reduce the root mean squared error to
17% of that from non-periodic models and 27% of the nearest rival approach
which is the resonator model.Comment: 61 pages, 13 figures, accepted for publication in JMLR. Updates from
earlier version occur throughout article in response to JMLR review
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